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Genome Additions Master Ticket #1470

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jennaj opened this Issue Jan 11, 2016 · 20 comments

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jennaj commented Jan 11, 2016

Genome and indexes for CVMFS and http://usegalaxy.org

CONVERT THIS ISSUE TO A PROJECT @jennaj

This list changes over time as new data sources are targetted for indexing and user requests are considered. See posts below for genome batches completed and in progress.

Current plans are to bring http://usegalaxy.org up to date with UCSC's released genomes, indexed for all tools, so those do not need to be requested by users at this time.

Main:

Other reference data:

Admin/Local Data and DM usage enhancements are included here.

  • #1471 -Methods to manage genomes, Admin enhancement ideas
  • #1516 -Sort view by dbkey Admin -> Local Data -> View Tool Data Table Entries
  • #1518 -Add dbkey to report and sort by it in Admin -> Local Data -> View Data Manager Jobs
  • galaxyproject/tools-devteam#319 -Modify Bowtie2 DM so that it will not create duplicates when "Include Tophat2" is used
  • galaxyproject/tools-iuc#530 -HISAT2 Data manager reports unrecognized arguments for SNP annotation
  • #1904 -LiftOver DM request

Resolved data issues:

New genomes and indexes will be installed at https://test.galaxyproject.org/ first for testing. If your genome is listed and checked as complete, community testing and feedback can be posted to https://biostar.usegalaxy.org or through a bug report from the error dataset (from a mapping tool, etc).

All data will later be promoted to http://usegalaxy.org. Timeline is not firm.

Making a Reference genome request

  • Create reply below
  • Be specific
    • Name of organism, including common "key" used
    • Exact source. Ex: UCSC (dbkey), NCBI project ID, other URL
    • Build details: include mito, chloro, plasmids, etc.
    • All indexes are now generated for brand new genomes by default. Or pick one of: "All" "Bowtie2" "MyFavTool" if your genome is at http://usegalaxy.org, but not available in your tool of interest
    • Don't forget anyone can add and use a custom genome right now with most tools - no waiting! https://wiki.galaxyproject.org/Learn/CustomGenomes
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jennaj commented Jan 12, 2016

For reference,

Master spreadsheet of dbkeys and indexes done and to-do. Older genomes removed.
https://docs.google.com/spreadsheets/d/1jtDC-2STroUINP6KVrfhZwGQgpP5y-HhkRMONZtD1W4/edit?usp=sharing

dbkeys with fasta loaded.
https://gist.github.com/jennaj/aeb8d6af4e4722a89f62d15af8ce3452

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jennaj commented Jan 14, 2016

Issues detected

Meets goal of consistency in nomeclature permiting DMs to function

change genome label in all_fasta (kill "full" in all descriptions/dbkeys). Other locs may need mods.

  • ci2full to ci2 (dbkey & description)
  • cb3full to cb3 (dbkey & description)
  • "panTro3 Full" to "panTro3" (description only, no "Canonical" exists)
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jennaj commented Mar 10, 2016

Genomes that need followup:

Not at http://genome.ucsc.edu (browser or download). Are at http://genome-test.cse.ucsc.edu/. Pending release?

  • rheMac7 Rhesus (in builds list, but that does not contain genome-test anymore. odd)
  • rheMac8 Rhesus (not in builds list, can be captured next update)
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jennaj commented Apr 11, 2016

Completed and indexes promoted to http://usegalaxy.org (Galaxy Main) April 2016

Fasta

New genomes (confirmed, to be indexed for all)

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish **not in builds list - created dbkey but did not populate to http://usegalaxy.org. Impact, all data (inc indexes) does not populate on mapping tools forms, etc) See #2530
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi not in builds list - created dbkey Same issue as danRer10.
  • felCat8 Cat

2bit

Note: Lastz indexes created by same DM

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi
  • felCat8 Cat

Existing

  • melUnd1 Budgerigar
  • bosTau7 Cow

Sam

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi
  • felCat8 Cat

Existing

Picard

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi
  • felCat8 Cat

Existing

Bowtie2/Tophat2

Issue about Bowtie2 DM creating duplicate indexes: galaxyproject/tools-devteam#319

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi
  • felCat8 Cat

Existing

  • galGal3 Chicken Full & Canonical
  • galGal4 Chicken
  • melGal1 Turkey
  • equCab1 Equus caballus
  • equCab2 Equus caballus
  • loxAfr1 African Elephant (duplicate in Bowtie2 - DM does not allow Tophat2 only creation - ticket)
  • loxAfr3 African Elephant
  • sacCer2 S. cerevisiae
  • sacCer3 S. cerevisiae
  • Schizosaccharomyces_pombe_1.1
  • rheMac2 Rhesus
  • rheMac3 Rhesus
  • eschColi_K12 Escherichia coli (str. K-12 substr. MG1655)
  • melUnd1 Budgerigar

BWA/BWA-MEM

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi (built using BWT-SW)
  • felCat8 Cat

Existing

  • equCab1 Equus caballus
  • equCab2 Equus caballus
  • sacCer2 S. cerevisiae
  • sacCer3 S. cerevisiae (created dup, needs cleanup)
  • Schizosaccharomyces_pombe_1.1
  • rheMac2 Rhesus
  • rheMac3 Rhesus
  • galGal3 Chicken (full) (built using BWT-SW)
  • galGal3 Canonical
  • galGal4 Chicken
  • melGal1 Turkey
  • loxAfr1 African Elephant
  • loxAfr3 African Elephant
  • bosTauMd3 Cow
  • ce9 C. elegans
  • susScr2 Pig
  • canFam2 Dog
  • canFam3 Dog
  • eschColi_K12 Escherichia coli (str. K-12 substr. MG1655)
  • papHam1 Baboon
  • melUnd1 Budgerigar (built using BWT-SW)
  • otoGar1 Bushbaby
  • otoGar3 Bushbaby
  • felCat5 Cat
  • panTro3 Chimpanzee Full & Canonical
  • panTro4 Chimpanzee
  • turTru2 Dolphin

HISAT2

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi
  • felCat8 Cat

Existing

  • hg38
  • hg38canon
  • hg38female
  • hg19
  • hg19canon
  • hg19female
  • hg19_rCRS_pUC18_phiX174
  • hg_g1k_v37 1000Genomes
  • mm10
  • mm9
  • dm3
  • equCab1 Equus caballus
  • equCab2 Equus caballus
  • sacCer2 S. cerevisiae
  • sacCer3 S. cerevisiae
  • Schizosaccharomyces_pombe_1.1
  • rheMac2 Rhesus
  • rheMac3 Rhesus
  • galGal3 Chicken Full & Canonical
  • galGal4 Chicken
  • melGal1 Turkey
  • loxAfr1 African Elephant
  • loxAfr3 African Elephant
  • ce9 C. elegans
  • ce10 C. elegans
  • susScr2 Pig
  • susScr3 Pig
  • bosTauMd3 Cow
  • bosTau7 Cow
  • canFam2 Dog
  • canFam3 Dog
  • eschColi_K12 Escherichia coli (str. K-12 substr. MG1655)
  • papHam1 Baboon
  • melUnd1 Budgerigar
  • otoGar1 Bushbaby
  • otoGar3 Bushbaby
  • felCat5 Cat
  • panTro3 Chimpanzee Full & Canonical
  • panTro4 Chimpanzee
  • turTru2 Dolphin

Liftover

See distinct tracking checklist, below

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jennaj commented Apr 11, 2016

2018

Fasta

New genomes (confirmed, to be indexed for all)

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

2bit

Note: Lastz indexes created by same DM

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • Arabidopsis_thaliana_TAIR10 (check if exists)
  • Add here

Sam

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • Add here

Picard

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • Add here

Bowtie2/Tophat2

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • danRer9 Zebrafish (double check if needed)

BWA/BWA-MEM

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • danRer9 Zebrafish
  • danRer10 Zebrafish

HISAT2

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • danRer9 Zebrafish
  • danRer10 Zebrafish

Liftover

See distinct tracking checklist, below

RNA STAR

Fast tracked genomes #1470 (comment)

New genomes

  • Arabidopsis_thaliana_TAIR10 (exists in all_fasta.loc, check others)
  • hg38Patch2 - (GRCh38.p2 Human) source NCBI or UCSC? Check chrom IDs in .len
  • anaPla1 Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1) - source UCSC test server
  • ce11 C. elegans Feb. 2013 (WBcel235/ce11)
  • criGri1 Chinese hamster
  • fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3)
  • galGal5 Dec 2015 (Gallus_gallus-5.0/galGal5)
  • latCha1 Coelacanth
  • oviAri3 Aug. 2012 (ISGC Oar_v3.1/oviAri3)
  • rheMac8 Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
  • susScr11 Pig Feb. 2017 (Sscrofa11.1/susScr11)

Existing

  • danRer9 Zebrafish
  • danRer10 Zebrafish

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jennaj commented Apr 11, 2016

New genomes under review (source/licence)

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jennaj commented Apr 25, 2016

Liftover

Needs DM: #1904

Workaround: Use the LiftOver tool at UCSC (the source for the wrapped version in Galaxy) and upload the results to Galaxy to use with other analysis. http://genome.ucsc.edu/cgi-bin/hgLiftOver

New genomes

  • rn6 Rat
  • dm6 Fruit Fly
  • musFur1 Ferret
  • cerSim1 White Rhino
  • nomLeu3 Gibbon
  • danRer10 Zebrafish
  • danRer9 Zebrafish (update)
  • bosTau8 Cow
  • papAnu2 Baboon
  • vicPac1 Alpaca
  • vicPac2 Alpaca
  • allMis1 American alligator
  • dasNov3 Armadillo
  • gadMor1 Atlantic cod
  • panPan1 Bonobo
  • aptMan1 Brown Kiwi
  • melUnd1 Budgerigar (only had .fa, sam, picard originally - odd)
  • felCat8 Cat
  • criGri1 Chinese hamster
  • latCha1 Coelacanth

Existing (update)

  • Probably all - need automated retrieval of new, ignore existing
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natefoo commented May 11, 2016

@jennaj I updated the April 2016 comment to include the missing BWA indexes that I was able to build with the BWT-SW algorithm.

Some (like galGal3 and panTro3) with full/canonical variants I rebuilt. The only difference from the original DM run is that after selecting the correct build from "Source FASTA Sequence", I put the build variant name (e.g. galGal3canon) in the "ID for sequence" field. Otherwise the builds clobber eachother in the index dir on disk (the "ID for sequence" field is used for naming the index subdirectory and defaults to the dbkey - which for both full and canonical builds is still just e.g. galGal3 - this could be a bit more intuitive in the DM, I had no idea what "ID for sequence" was for until I noticed that two loc file entries pointed to the same directory/indexes on disk and then dug into the DM code to understand it). I rebuilt these for any indexes which had the variants built originally, and cleaned up the old directories and their entries in the location files.

These BWA indexes and the rest of the indexes in that comment are now in the process of being published to CVMFS and once done (this may take a long time) will be available on usegalaxy.org (after a restart, I'll comment again when it's all ready).

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natefoo commented May 11, 2016

@jennaj The publishing is finished and Main has been restarted.

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jennaj commented May 18, 2016

Add hg38 MAF alignments. Request: https://biostar.usegalaxy.org/p/17690

@jennaj jennaj changed the title Early 2016 Genome Additions 2016 Genome Additions Jul 14, 2016

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massaali commented Oct 8, 2016

Hello,

I saw 7 weeks ago that another user had made this same request for a newer version of the sheep reference genome - you currently have OviAri1 which is 6 years old and there are two newer versions (about to be 3 newer versions) could we get a newer version? Sheep are amazing agricultural species important for meat milk and wool production and more researchers should study them! I request the current version on NCBI/ENSEMBL for all tools Bowtie and mapping tools, and chIP-seq, RNA-seq tools too: Ovis aries Oar_v4.0 its from late 2015.

Thank you for considering!

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sayalih commented Oct 9, 2016

Hi

I think the best way to is to use your genome of interest - use the fasta
format and upload it on galaxy using firezilla. And there is an option to
align with your uploaded sequence instead of the reference genome.
Links to how to do this:
https://wiki.galaxyproject.org/Support#Custom_reference_genome

I don't think they are uploading any more reference genomes on their
default list.

Sayali.


Update by @jennaj: Yes, use a custom reference genome for now. I will add in sheep and other requests to the next list of updates #1470 (comment)

@jennaj jennaj changed the title 2016 Genome Additions Genome Additions Master Ticket Oct 25, 2016

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vebaev commented Jan 25, 2017

It will be great if you include the tomate 2.40 genome from:
ftp://ftp.solgenomics.net/tomato_genome/
And pepper C.annuum_cvCM334 from:
ftp://ftp.solgenomics.net/genomes/Capsicum_annuum/C.annuum_cvCM334/

@jennaj Yes, they are in NCBI (tomato and pepper):
https://www.ncbi.nlm.nih.gov/genome/7
https://www.ncbi.nlm.nih.gov/genome/10896

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jennaj commented Jun 9, 2017

Priority indexes

RNA STAR



Indexes

  • hg38
  • hg19
  • mm10
  • mm9
  • rn6
  • rn5
  • dm6
  • dm3
  • sacCer3
  • sacCer2
  • ce9
  • ce10

Future requests (may be moved to a new post in this same issue)

  • bosTau8
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iraplee commented Jun 12, 2017

We're looking for X. tropicalus index to be uploaded to HiSat2

xenTro1 xenTro1 Frog (Xenopus tropicalis): xenTro1 /galaxy/data/xenTro1/seq/xenTro1.fa
xenTro2 xenTro2 Frog (Xenopus tropicalis): xenTro2 /galaxy/data/xenTro2/seq/xenTro2.fa
xenTro3 xenTro3 Frog (Xenopus tropicalis): xenTro3 /galaxy/data/xenTro3/seq/xenTro3.fa

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bimbam23 commented Jun 27, 2017

New Pig genome:
Sus Scrofa 11.1, susscr4
NCBI GCF_000003025.6
all: (chr and chrUn plus chrMT)

genome:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz
gff3:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.gff.gz

lookup table nice names: https://test.galaxyproject.org/u/bickj/h/pig-genome-lookup-table

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PseudomonasP commented Nov 21, 2017

Dear Galaxy Team,
I hope this is still the right place to request genome additions.

If we could get Brassica napus (Bna) as a built-in genome, that would be amazing:
http://www.genoscope.cns.fr/brassicanapus/data/

Please note that although the annotation is titled v5 while the genome itself is v4.1, it should work just fine, as we have had no problems with it.

@martenson martenson referenced this issue Dec 11, 2017

Closed

The Roadmap #1928

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@jennaj jennaj referenced this issue Jan 20, 2018

Open

Update Kraken reference data #80

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@jennaj jennaj referenced this issue Feb 8, 2018

Closed

Data fixes to-do summarized #55

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jennaj commented May 1, 2018

Add NCBI's Xenopus laevis and Xenopus tropicalis genomes (indexed for all tools).

The genome is at https://usegalaxy.eu -- so when we get the data synced between all mirrors that might be the best solution.

Request: https://biostar.usegalaxy.org/p/27778

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jennaj commented Nov 26, 2018

Request: add Medicago truncatula https://biostar.usegalaxy.org/p/5916/#30132

To-do: Check if present in ELIXER plant genomes already indexed (to be added in cvmfs): https://www.elixir-europe.org/about/groups/galaxy-wg

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jennaj commented Jan 29, 2019

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