ggd search¶
[Click here to return to the home page]
ggd search is used to search for a data package stored within the ggd ecosystem. It is dependent on the ggd channel provided.
Using ggd search¶
Once ggd is installed on your system you can run ggd search to search for available data packages.
Running ggd search -h will give you the a similar help message as below:
Search arguments:
ggd search |
Search for available ggd data packages. Results are filtered by match score from high to low. (Only 5 results will be reported unless the -dn flag is changed) |
|---|---|
|
show this help message and exit |
|
Required The term(s) to search for. Multiple terms can be used. Example: ‘ggd search reference genome’, where “reference” and “genome” are the search terms |
|
(Optional) How to search for data packages with the search terms provided. Options = ‘combined-only’, ‘non-combined-only’, and ‘both’. ‘combined-only’ will use the provided search terms as a single search term. ‘non-combined-only’ will use the provided search terms to search for data package that match each search term separately. ‘both’ will use the search terms combined and each search term separately to search for data packages. Default = ‘both’ |
|
(Optional) Filter results by the genome build of the desired recipe |
|
(Optional) Filter results by the species for the desired recipe |
|
(Optional) The number of search results to display. (Default = 5) |
|
(Optional) A score between 0 and 100 to use to filter the results by. (Default = 75). The lower the number the more results will be output” |
|
(Optional) The ggd channel to search. (Default = genomics) |
Any combination of search terms can be used to search for a package.
Additional argument explanation:¶
Required arguments:
search_term: The
search_termis a positional argument that represents the “terms” to search for. At least one search term is required, but multiple can be provided NOTE: You do not need to add the keywordsearch_term.
Note
If the genome build or the species is added to the search terms the results will be filtered based on the species and/or genome build provided. (The genome build and/or species
need to be spelled the same as the choices for the -g or -s flags
Optional arguments:
–search-type The
--search-typeflag is used to set search term combination filtering. There are three options. (1) Search forcombined-onlymatches, meaning search for packages when the search terms are combined as a single search term. (2) Search fornon-combined-onlymatches, meaning search for packages where each term is used as a separate search term. (3) Search forbothcombined and non-combined matches, meaning do both (1) and (2). The default behavior is set toboth.-g: The
-gflag is used to filter the search results on a specific “genome build”. This flag is not required, however, if provided the resulting search will be filtered to only include data packages with that genome build.-s: The
-sflag is used to filter the search results on a specific “species”. Only data packages for that specific species will be displayed.-dn: The
-dnflag is used to filter the search results based on the number of results to display. Default = 5. If more than 5 results are available and you don’t see the desired package in the results list, add the-dn {N}flag where N is the number of results to show.-m: The
-mflag represents the “match” score to use for searching. A fuzzy word match is used to identify similar packages to the terms search for, and the match score defines which packages will be displayed based on a cutoff. A default match score cutoff is provided, but this flag can be used to provide more strict or more lenient search results. (Default = 75)-c: The
-cflag is used to set the ggd channel to search in. The genomics channel is set by default.Note
There is no limit to the number of search terms you can use. However, the more search terms used will result in an increase in the number of results returned.
Additionally, the genome build or species can be used as a search term. If they are spelled correctly, regardless of case, the results will be filtered by that genome build and/or species. If a genome build or species is added as a search term and is not spelled correctly the results will NOT be filtered by the intended genome build and/or species.
Example¶
Some examples of using the ggd search tool:
1. Simple example with one search term:¶
$ ggd search reference
----------------------------------------------------------------------------------------------------
mm10-reference-ucsc-v1
======================
Summary: Reference genome for mouse from UCSC
Species: Mus_musculus
Genome Build: mm10
Keywords: reference, ucsc, mouse, mm10, reference-genome, fasta-file
Data Version: 07-Feb-2012
To install run:
ggd install mm10-reference-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-reference-genome-ucsc-v1
=============================
Summary: The hg19 soft masked genomic DNA seqeunce reference genome from UCSC (patch 13). Repeats found by 'RepeatMasker' and 'Tandem Repeat Finder' are shown as lower case. Non repeating seqeunce are shown as upper case.
Species: Homo_sapiens
Genome Build: hg19
Keywords: ref, reference-genome, fasta-file, soft-masked
Data Provider: UCSC
Data Version: 17-Jan-2020
File type(s): fa
Data file coordinate base: NA
Included Data Files:
hg19-reference-genome-ucsc-v1.fa.gz
hg19-reference-genome-ucsc-v1.fa.gz.fai
hg19-reference-genome-ucsc-v1.fa.gz.gzi
Approximate Data File Sizes:
hg19-reference-genome-ucsc-v1.fa.gz: 997.23M
hg19-reference-genome-ucsc-v1.fa.gz.fai: 12.23K
hg19-reference-genome-ucsc-v1.fa.gz.gzi: 808.71K
To install run:
ggd install hg19-reference-genome-ucsc-v1
----------------------------------------------------------------------------------------------------
hg38-reference-genome-ucsc-v1
=============================
Summary: The hg38 soft masked genomic DNA seqeunce reference genome from UCSC (patch 12). Repeats found by 'RepeatMasker' and 'Tandem Repeat Finder' are shown as lower case. Non repeating seqeunce are shown as upper case.
Species: Homo_sapiens
Genome Build: hg38
Keywords: ref, reference-genome, fasta-file, soft-masked
Data Provider: UCSC
Data Version: 10-Aug-2018
File type(s): fa
Data file coordinate base: NA
Included Data Files:
hg38-reference-genome-ucsc-v1.fa.gz
hg38-reference-genome-ucsc-v1.fa.gz.fai
hg38-reference-genome-ucsc-v1.fa.gz.gzi
Approximate Data File Sizes:
hg38-reference-genome-ucsc-v1.fa.gz: 1.02G
hg38-reference-genome-ucsc-v1.fa.gz.fai: 25.61K
hg38-reference-genome-ucsc-v1.fa.gz.gzi: 814.34K
To install run:
ggd install hg38-reference-genome-ucsc-v1
----------------------------------------------------------------------------------------------------
grch37-reference-genome-1000g-v1
================================
Summary: GRCh37 reference genome from 1000 genomes
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: ref, reference, fasta-file
Data Version: phase2_reference
To install run:
ggd install grch37-reference-genome-1000g-v1
----------------------------------------------------------------------------------------------------
hg19-reference-genome-gencode-v1
================================
Summary: The GRCh37 DNA nucleotide sequence primary assembly. Sequence regions include reference chromosomes and scaffoldings. Mapped to hg19
Species: Homo_sapiens
Genome Build: hg19
Keywords: Reference-Genome, Fasta, DNA-Sequence, GENCODE-34, Fasta-sequence, primary-assembly
Data Provider: GENCODE
Data Version: release-34
File type(s): fa
Data file coordinate base: NA
Included Data Files:
hg19-reference-genome-gencode-v1.fa.gz
hg19-reference-genome-gencode-v1.fa.gz.fai
hg19-reference-genome-gencode-v1.fa.gz.gzi
Approximate Data File Sizes:
hg19-reference-genome-gencode-v1.fa.gz: 881.99M
hg19-reference-genome-gencode-v1.fa.gz.fai: 2.82K
hg19-reference-genome-gencode-v1.fa.gz.gzi: 772.92K
To install run:
ggd install hg19-reference-genome-gencode-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
************************************
Package Name Results
====================
mm10-reference-ucsc-v1
hg19-reference-genome-ucsc-v1
hg38-reference-genome-ucsc-v1
grch37-reference-genome-1000g-v1
hg19-reference-genome-gencode-v1
grch37-reference-genome-gencode-v1
NOTE: Name order matches order of packages in detailed section above
************************************
:ggd:search: NOTE Only showing results for top 5 of 30 matches.
:ggd:search: To display all matches append your search command with '-dn 30'
ggd search reference -dn 30
2. Simple example with two search terms:¶
$ ggd search chrom sizes
----------------------------------------------------------------------------------------------------
hg19-chromsizes-ggd-v1
======================
Summary: Chromosome lengths for hg19
Species: Homo_sapiens
Genome Build: hg19
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-Apirl-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
hg19-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
hg19-chromsizes-ggd-v1.txt: 1.99K
To install run:
ggd install hg19-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
hg38-chromsizes-ggd-v1
======================
Summary: Chromosome lengths for hg38
Species: Homo_sapiens
Genome Build: hg38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-Apirl-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
hg38-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
hg38-chromsizes-ggd-v1.txt: 15.53K
To install run:
ggd install hg38-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch37-chromsizes-ggd-v1
========================
Summary: Chromosome lengths for GRCh37
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-Apirl-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
grch37-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch37-chromsizes-ggd-v1.txt: 5.17K
To install run:
ggd install grch37-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch38-chromsizes-ggd-v1
========================
Summary: Chromosome lengths for GRCh38
Species: Homo_sapiens
Genome Build: GRCh38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-April-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
grch38-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch38-chromsizes-ggd-v1.txt: 11.14K
To install run:
ggd install grch38-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
***************************
Package Name Results
====================
hg19-chromsizes-ggd-v1
hg38-chromsizes-ggd-v1
grch37-chromsizes-ggd-v1
grch38-chromsizes-ggd-v1
NOTE: Name order matches order of packages in detailed section above
***************************
:ggd:search: NOTE: Only showing results for top 5 of 22 matches.
:ggd:search: To display all matches append your search command with '-dn 22'
ggd search chrom sizes -dn 22
3. Simple example with the genome build as a search term:¶
$ ggd search repeat masker hg19
----------------------------------------------------------------------------------------------------
hg19-repeatmasker-ucsc-v1
=========================
Summary: RepeatMasker track from UCSC in bed format. Interspersed repeats and low complexity sequences identified using the RepeatMasker program. Scaffoldings missing from the GGD hg19.genome file are removed.
Species: Homo_sapiens
Genome Build: hg19
Keywords: rmsk, region, low-complexity-repeats, SINE, ALUs, LINE, LTR, DNA-repeat-elements, simple-repeats, RNA-repeats
Data Provider: UCSC
Data Version: 22-Mar-2020
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
hg19-repeatmasker-ucsc-v1.bed.gz
hg19-repeatmasker-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-repeatmasker-ucsc-v1.bed.gz: 114.62M
hg19-repeatmasker-ucsc-v1.bed.gz.tbi: 526.98K
To install run:
ggd install hg19-repeatmasker-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-simple-repeats-ucsc-v1
===========================
Summary: Simple repeats track from UCSC. Simple tandem repeats and imperfect repeats identified by the Tandem Repeats Finder (TRF) algorithm. Any scaffoldings not in the hg19.genome file are removed from the final file
Species: Homo_sapiens
Genome Build: hg19
Keywords: simrep, simple-repeats, repeats, tandem-repeats, simple-tandem-repeats
Data Provider: UCSC
Data Version: 22-Mar-2020
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
hg19-simple-repeats-ucsc-v1.bed.gz
hg19-simple-repeats-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-simple-repeats-ucsc-v1.bed.gz: 25.58M
hg19-simple-repeats-ucsc-v1.bed.gz.tbi: 1.35M
To install run:
ggd install hg19-simple-repeats-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-microsatellites-ucsc-v1
============================
Summary: Microsatellites from UCSC. Region which tend to be highly polymorphic and with at least 15 di- or tri-nucletodie repeats
Species: Homo_sapiens
Genome Build: hg19
Keywords: microsatellites, microsats, STR, STRs, short-tandem-repeat, repeats, repeat-regions
Data Provider: UCSC
Data Version: 28-Nov-2010
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
hg19-microsatellites-ucsc-v1.bed.gz
hg19-microsatellites-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-microsatellites-ucsc-v1.bed.gz: 401.08K
hg19-microsatellites-ucsc-v1.bed.gz.tbi: 298.03K
To install run:
ggd install hg19-microsatellites-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-self-chain-ucsc-v1
=======================
Summary: Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC.
Species: Homo_sapiens
Genome Build: hg19
Keywords: Self-Chain, Self-Alignment, Repeats, low-copy-repeats
Data Provider: UCSC
Data Version: 27-Apr-2009
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
hg19-self-chain-ucsc-v1.bed.gz
hg19-self-chain-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-self-chain-ucsc-v1.bed.gz: 21.74M
hg19-self-chain-ucsc-v1.bed.gz.tbi: 201.69K
To install run:
ggd install hg19-self-chain-ucsc-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
******************************
Package Name Results
====================
hg19-repeatmasker-ucsc-v1
hg19-simple-repeats-ucsc-v1
hg19-microsatellites-ucsc-v1
hg19-self-chain-ucsc-v1
NOTE: Name order matches order of
******************************
4. Example using -g and -s flags to filter the results:¶
$ ggd search autosomal-dominant -g GRCh37 -s Homo_sapiens
----------------------------------------------------------------------------------------------------
grch37-autosomal-dominant-genes-berg-v1
=======================================
Summary: CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes (as of June 2011) deemed to follow autosomal dominant inheritance. (Assembled by Macarthur Lab). Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991).
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genes, autosomal-dominant, disease, Berg_et_al, AD, OMIM, gene_coordinates, CDS-regions
Data Provider: berg
Data Version: 1-15-2013
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
grch37-autosomal-dominant-genes-berg-v1.bed.gz
grch37-autosomal-dominant-genes-berg-v1.bed.gz.tbi
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz.tbi
Approximate Data File Sizes:
grch37-autosomal-dominant-genes-berg-v1.bed.gz: 119.97K
grch37-autosomal-dominant-genes-berg-v1.bed.gz.tbi: 27.12K
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz: 73.13K
grch37-autosomal-dominant-genes-berg-v1.compliment.bed.gz.tbi: 20.39K
To install run:
ggd install grch37-autosomal-dominant-genes-berg-v1
----------------------------------------------------------------------------------------------------
grch37-autosomal-dominant-genes-blekhman-v1
===========================================
Summary: CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes deemed to follow autosomal dominant inheritance according to extensive manual curation by Molly Przeworski's group.(https://www.ncbi.nlm.nih.gov/pubmed/18571414).
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genes, autosomal-dominant, disease, Blekhman_et_al, AD, OMIM, gene_coordinates, CDS-regions
Data Provider: blekhman
Data Version: 6-24-2008
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz.tbi
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz.tbi
Approximate Data File Sizes:
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz: 59.94K
grch37-autosomal-dominant-genes-blekhman-v1.bed.gz.tbi: 15.15K
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz: 38.45K
grch37-autosomal-dominant-genes-blekhman-v1.compliment.bed.gz.tbi: 15.37K
To install run:
ggd install grch37-autosomal-dominant-genes-blekhman-v1
----------------------------------------------------------------------------------------------------
grch37-autosomal-dominant-genes-berg-blekhman-v1
================================================
Summary: CDS region genomic coordinates, along with the compliment coordinates, for combined set of OMIM disease genes deemed to follow autosomal dominant inheritance. (Assembled by Macarthur Lab). Gene sets from: Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991). Blekham et al, 2008: (https://www.ncbi.nlm.nih.gov/pubmed/18571414)
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genes, autosomal-dominant, disease, Berg_et_al, Blekhman_et_al, AD, OMIM, gene_coordinates, CDS-regions
Data Provider: berg-blekhman
Data Version: 1-15-2013_6-24-2008
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz.tbi
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz.tbi
Approximate Data File Sizes:
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz: 135.22K
grch37-autosomal-dominant-genes-berg-blekhman-v1.bed.gz.tbi: 29.55K
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz: 83.03K
grch37-autosomal-dominant-genes-berg-blekhman-v1.compliment.bed.gz.tbi: 21.44K
To install run:
ggd install grch37-autosomal-dominant-genes-berg-blekhman-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
**************************************************
Package Name Results
====================
grch37-autosomal-dominant-genes-berg-v1
grch37-autosomal-dominant-genes-blekhman-v1
grch37-autosomal-dominant-genes-berg-blekhman-v1
NOTE: Name order matches order of packages in detailed section above
**************************************************
5. Example of searching for two different data packages at the same time for a specific genome build¶
The default behavior is to search for terms both combine and separately. Therefore, one does noes need
to set the --search-type unless they would like to refine the results. The example below can also
be done with setting search-type flag as such: --search type non-combined-only
$ ggd search pfam cpg hg19
----------------------------------------------------------------------------------------------------
hg19-pfam-domains-ucsc-v1
=========================
Summary: High quality, manually curated Pfam domain annotation in bed12 format from UCSC
Species: Homo_sapiens
Genome Build: hg19
Keywords: pfam, domains, protein, protein-domains, UCSC
Data Provider: UCSC
Data Version: 16-Apr-2017
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
hg19-pfam-domains-ucsc-v1.bed12.bed.gz
hg19-pfam-domains-ucsc-v1.bed12.bed.gz.tbi
Approximate Data File Sizes:
hg19-pfam-domains-ucsc-v1.bed12.bed.gz: 1.41M
hg19-pfam-domains-ucsc-v1.bed12.bed.gz.tbi: 143.50K
To install run:
ggd install hg19-pfam-domains-ucsc-v1
----------------------------------------------------------------------------------------------------
hg19-cpg-islands-ucsc-v1
========================
Summary: cpg islands from UCSC in bed format. Scaffoldings that are not contained in the hg19.genome file are removed
Species: Homo_sapiens
Genome Build: hg19
Keywords: CpG, region, bed-file, cpg-islands, islands
Data Provider: UCSC
Data Version: 22-Mar-2020
File type(s): bed
Data file coordinate base: 0-based-inclusive
Included Data Files:
hg19-cpg-islands-ucsc-v1.bed.gz
hg19-cpg-islands-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-cpg-islands-ucsc-v1.bed.gz: 621.35K
hg19-cpg-islands-ucsc-v1.bed.gz.tbi: 186.06K
To install run:
ggd install hg19-cpg-islands-ucsc-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
***************************
Package Name Results
====================
hg19-pfam-domains-ucsc-v1
hg19-cpg-islands-ucsc-v1
NOTE: Name order matches order of packages in detailed section above
***************************
6. Example refining search results based on combined terms¶
In this example the --search-term flag is set to combined-only. This is often done when you know which
package you want but don’t know the exact package name. This will refine the results to those based on a combination
of the terms provided.
ggd search chrom sizes --search-type combined-only -dn 8
----------------------------------------------------------------------------------------------------
grch37-chromsizes-ggd-v1
========================
Summary: Chromosome lengths for GRCh37
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-Apirl-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
grch37-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch37-chromsizes-ggd-v1.txt: 5.17K
To install run:
ggd install grch37-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch37-chromsizes-ncbi-v1
=========================
Summary: Chromosome lengths for the GRCh37 genome build from NCBI. (Used to create the Go Get Data (GGD) GRCh37.genome file)
Species: Homo_sapiens
Genome Build: GRCh37
Keywords: genome, chromosome, lengths, sizes, chrom-lengths
Data Provider: NCBI
Data Version: 12-October-2016-(patch13)
File type(s): genome
Data file coordinate base: NA
Included Data Files:
grch37-chromsizes-ncbi-v1.genome
Approximate Data File Sizes:
grch37-chromsizes-ncbi-v1.genome: 5.17K
To install run:
ggd install grch37-chromsizes-ncbi-v1
----------------------------------------------------------------------------------------------------
grch38-chromsizes-ggd-v1
========================
Summary: Chromosome lengths for GRCh38
Species: Homo_sapiens
Genome Build: GRCh38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-April-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
grch38-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
grch38-chromsizes-ggd-v1.txt: 11.14K
To install run:
ggd install grch38-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
grch38-chromsizes-ncbi-v1
=========================
Summary: Chromosome lengths for the GRCh38 genome build from NCBI. (Used to create the Go Get Data (GGD) GRCh38.genome file)
Species: Homo_sapiens
Genome Build: GRCh38
Keywords: genome, chromosome, lengths, sizes, chrom-lengths
Data Provider: NCBI
Data Version: 14-April-2020-(patch13)
File type(s): genome
Data file coordinate base: NA
Included Data Files:
grch38-chromsizes-ncbi-v1.genome
Approximate Data File Sizes:
grch38-chromsizes-ncbi-v1.genome: 11.14K
To install run:
ggd install grch38-chromsizes-ncbi-v1
----------------------------------------------------------------------------------------------------
hg19-chromsizes-ggd-v1
======================
Summary: Chromosome lengths for hg19
Species: Homo_sapiens
Genome Build: hg19
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-Apirl-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
hg19-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
hg19-chromsizes-ggd-v1.txt: 1.99K
To install run:
ggd install hg19-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
hg19-chromsizes-ncbi-v1
=======================
Summary: Chromosome lengths for the hg19 genome build from NCBI. (Used to create the Go Get Data (GGD) hg19.genome file)
Species: Homo_sapiens
Genome Build: hg19
Keywords: genome, chromosome, lengths, sizes, chrom-lengths
Data Provider: NCBI
Data Version: 12-October-2016-(patch13)
File type(s): genome
Data file coordinate base: NA
Included Data Files:
hg19-chromsizes-ncbi-v1.genome
Approximate Data File Sizes:
hg19-chromsizes-ncbi-v1.genome: 1.99K
To install run:
ggd install hg19-chromsizes-ncbi-v1
----------------------------------------------------------------------------------------------------
hg38-chromsizes-ggd-v1
======================
Summary: Chromosome lengths for hg38
Species: Homo_sapiens
Genome Build: hg38
Keywords: genome, chromosome, lengths, sizes
Data Provider: GGD
Data Version: 16-Apirl-2020
File type(s): txt
Data file coordinate base: NA
Included Data Files:
hg38-chromsizes-ggd-v1.txt
Approximate Data File Sizes:
hg38-chromsizes-ggd-v1.txt: 15.53K
To install run:
ggd install hg38-chromsizes-ggd-v1
----------------------------------------------------------------------------------------------------
hg38-chromsizes-ncbi-v1
=======================
Summary: Chromosome lengths for the hg38 genome build from NCBI. (Used to create the Go Get Data (GGD) hg38.genome file)
Species: Homo_sapiens
Genome Build: hg38
Keywords: genome, chromosome, lengths, sizes, chrom-lengths
Data Provider: NCBI
Data Version: 14-April-2020-(patch13)
File type(s): genome
Data file coordinate base: NA
Included Data Files:
hg38-chromsizes-ncbi-v1.genome
Approximate Data File Sizes:
hg38-chromsizes-ncbi-v1.genome: 15.53K
To install run:
ggd install hg38-chromsizes-ncbi-v1
----------------------------------------------------------------------------------------------------
>>> Scroll up to see package details and install info <<<
***************************
Package Name Results
====================
grch37-chromsizes-ggd-v1
grch37-chromsizes-ncbi-v1
grch38-chromsizes-ggd-v1
grch38-chromsizes-ncbi-v1
hg19-chromsizes-ggd-v1
hg19-chromsizes-ncbi-v1
hg38-chromsizes-ggd-v1
hg38-chromsizes-ncbi-v1
NOTE: Name order matches order of packages in detailed section above
***************************