iGenomes Change Log 04/12/18 -- Added new genome S. scrofa, Ensembl, Sscrofa11.1. 02/27/17 -- Added new genome G. gallus, UCSC, galGal5. 03/03/16 -- Made the mitochondrial chromosome name in genes.gtf and refFlat.txt.gz consistent for: Z. mays, Ensembl, AGPv2 Z. mays, Ensembl, AGPv3 D. melanogaster, Ensembl, BDGP5.25 D. melanogaster, Ensembl, BDGP5 D. melanogaster, Ensembl, BDGP6 S. cerevisiae, Ensembl, EF2 S. cerevisiae, Ensembl, EF3 S. cerevisiae, Ensembl, EF4 S. cerevisiae, Ensembl, R64-1-1 12/15/15 -- Added missing chr29 to: B. taurus, UCSC, bosTau6 B. taurus, UCSC, bosTau7 B. taurus, UCSC, bosTau8 08/26/15 -- Updated genome.dict and GenomeSize.xml for the following builds (species, source, build): H. sapiens, NCBI, GRCh38 H. sapiens, NCBI, GRCh38Decoy 08/18/15 -- Added the following new builds (species, source, build): H. sapiens, NCBI, GRCh38 H. sapiens, NCBI, GRCh38Decoy H. sapiens, UCSC, hg38 07/28/15 -- Added the following new builds (species, source, build): B. taurus, NCBI, UMD_3.1.1 B. taurus, UCSC, bosTau8 D. melanogaster, Ensembl, BDGP6 D. melanogaster, UCSC, dm6 D. rerio, Ensembl, GRCz10 D. rerio, NCBI, GRCz10 D. rerio, UCSC, danRer10 R. norvegicus, Ensembl, Rnor_6.0 R. norvegicus, NCBI, Rnor_6.0 R. norvegicus, UCSC, rn6 07/28/15 -- Fixed symlinks Genes and SmallRNA so they point to folders in Archives/archive-current for Z. mays, Ensembl, AGPv3 O. sativa_japonica, Ensembl, IRGSP-1.0 S. cerevisiae, Ensembl, R64-1-1 C. elegans, Ensembl, WBcel235 G. gallus, Ensembl, Galgal4 07/24/15 -- Updated gene annotation for all iGenomes. 05/21/15 -- Added snp142.vcf to H. sapiens, UCSC, hg19. 03/13/15 -- Added dbsnp142 to Human, UCSC, hg19 12/05/14 -- Added list of methylation sites to human, NCBI, build36.3 and build37.1. 06/10/14 -- Updated all GenomeSize.xml files to include the genome's name: genus species individual (source build). 06/06/14 -- Added MDSBowtieIndex to Homo sapiens, UCSC, hg19 for smallRNA analysis. 05/28/14 -- Added the following new builds (species, source, build): C. elegans, Ensembl, WBcel235 G. gallus, Ensembl, Galgal4 O. sativa japonica, Ensembl, IRGSP-1.0 S. cerevisiae, Ensembl, R64-1-1 Z. mays, Ensembl, AGPv3 05/27/14 -- Updated gene annotation for all iGenomes. Removed GenomeStudio directories and Squashed references for all iGenomes. 02/27/14 -- Fixed bug with mitochondrial chromosome name (was MT, now MtDNA) in C. elegans, Ensembl, all builds. Names are now consistent with annotation files. 03/25/13 -- Updated gene annotation for all genomes. 03/25/13 -- Added the following new builds (species, source, build): Ensembl: Canis_familiaris Ensembl CanFam3.1 Mus_musculus Ensembl GRCm38 Sus_scrofa Ensembl Sscrofa10.2 Rattus_norvegicus Ensembl Rnor_5.0 Schizosaccharomyces_pombe Ensembl (same build but added chrs MTR and AB325691) C_elegans Ensembl WBcel215 UCSC: Gallus_gallus UCSC galGal4 Pan_troglodytes UCSC panTro3 Pan_troglodytes UCSC panTro4 Bos_taurus UCSC bosTau6 Bos_taurus UCSC bosTau7 Canis_familiaris UCSC canFam3 Sus_scrofa UCSC susScr3 Rattus_norvegicus UCSC rrn5 NCBI: Drosophila_melanogaster NCBI build5.3 Drosophila_melanogaster NCBI build5.41 Mus_musculus NCBI GRCm38 Rattus_norvegicus NCBI Rnor_5.0 03/25/13 -- Added new species zebrafish - Danio rerio Danio_rerio Ensembl Zv9 Danio_rerio UCSC danRer7 Danio_rerio NCBI Zv9 03/25/13 -- Added dbsnp137 to Human, UCSC, hg19. 03/25/13 -- Added ribosomal sequences to all yeast (Saccharomyces_cerevisiae) genomes. 03/25/13 -- Added 18S ribosomal DNA sequence to NCBI genomes of Homo_sapiens, Mus_musculus, and Rattus_norvegicus in the file Annotation/Genes/ribosomalDNA.fa 05/24/12 -- Added new mouse build: species Mus_musculus, source UCSC, build mm10. 04/12/12 -- Added Bowtie2 indexes to all genomes (in Bowtie2Index directory). 03/14/12 -- Updated all gene annotation, small RNA sequences, and variation annotation files. 03/14/12 -- Reordered chromosome order of human genomes to support GATK chromosome ordering. 03/14/12 -- Added the following new builds (species, source, build): Bos taurus, Ensembl, UMD3.1 (note Ensembl is now supporting this build instead of Btau_4.0) Drosophila melanogaster, Ensembl, BDGP5 Escherichia_coli_K_12_DH10B, Ensembl, EB1 Pan troglodytes, Ensembl, CHIMP2.1.4 Saccharomyces cerevisiae, Ensembl, EF4 Schizosaccharomyces pombe, Ensembl, EF2 Caenorhabditis elegans, UCSC, ce10 Saccharomyces cerevisiae, UCSC, sacCer3 Arabidopsis thaliana, NCBI, TAIR10 Bos taurus, NCBI, Btau4.6.1 Canis_familiaris, NCBI, build3.1 Gallus gallus, NCBI, Build3.1 Sus scrofa, NCBI, Sscrofa10.2 Saccharomyces cerevisiae, NCBI, build3.1 03/14/12 -- Renamed B. subtilis, Ensembl, EB2 chromosome from 'chr' to 'Chromosome' in order to match gene annotation naming. 03/14/12 -- Added new BWA index format for BWA versions 0.6 and above. This is supported for all genomes. Also maintaining older version format (v0.5.x) in a separate directory. 03/14/12 -- Renamed picard dictionary files from genome.fa.dict to genome.dict in order to support GATK. 03/14/12 -- Added gene annotation file format refFlat.txt.gz to NCBI genomes in order to support picard CollectRnaSeqMetrics. All genomes that have available gene annotation should now have a refFlat.txt.gz file. 03/14/12 -- Changed the order of GTF file attributes to begin with 'gene_id' and 'transcript_id'. 03/14/12 -- Removed genome_size.xml file from UCSC and Ensembl genome since this file is now generated by CASAVA v1.7 and v1.8. 02/28/12 -- Added variations files for cow and pig from Ensembl. 02/09/12 -- Added B. subtilis genome -- species Bacillus_subtilis_168, source Ensembl, build EB2. 12/02/11 -- Added Soybean genome -- species Glycine max, source Ensembl, build Gm01. 11/11/11 -- Added Rhesus macaque genome -- species Macaca mulatta, source Ensembl, build Mmul_1. 11/01/11 -- Added dbsnp builds 128-130 to Human UCSC hg18. 08/30/11 -- Updated all gene annotation, small RNA sequences, and variation annotation files. 08/30/11 -- Added new Ensembl build Yeast (S. cerevisiae) EF3. Added new NCBI builds Chimp build3.1, Fly (D. melanogaster) build5.3, Mouse build37.2, Pig Sscrofa10, and Worm (C. elegans) WS195. 08/30/11 -- Added enterobacteriophage lambda genome from NCBI. 08/30/11 -- Added BWA index in new Sequence/BWAIndex directory for all iGenomes. 08/30/11 -- Added samtools index and picard dictionary in Sequence/WholeGenomeFasta folder for all iGenomes. 08/30/11 -- Modified all GTF files by adding tss_id (transcription start site id) and p_id (coding sequence id) attributes for use with Cufflinks. 08/30/11 -- Added D. melanogaster ribosomal sequences to AbundantSequences directories. 07/15/11 -- Added variation data for Human Ensembl GRCh37, Mouse Ensembl NCBIM37, Mouse NCBI build37.1, Mouse UCSC mm9, Rat Ensembl RGSC3.4, Rat NCBI RGSC_v3.4, and Rat UCSC rn4. 06/27/11 -- Added dbsnp build 132 data to Human UCSC hg19. 04/27/11 -- Removed genome_size.xml files in NCBI genomes, as chromosome names that begin with digits are not allowed in XML tags. 04/17/11 -- Changed all NCBI chromosome names from having a ‘c’ prefix to no prefix (eg, ‘c22’ to ‘22’). This is the native NCBI naming convention, and is needed for RNA workflows in CASAVA v1.8. 04/17/11 -- All NCBI genomes with gene annotation files now have a seq_gene.md.gz file downloaded unaltered from NCBI. A new file seq_gene.group_label.txt contains the seq_gene group label needed for parsing the primary assembly. 04/17/11 -- Changed all AbundantSequences fasta files to single-entry, since CASAVA v1.8 no longer allows multi-fasta files. 04/17/11 -- Renamed mitochondrial chromosomes from Human NCBI builds 37.1 and 37.2 from ‘Mt’ to ‘MT’. This change makes the names consistent with all other NCBI mitochondrial chromosomes in the iGenomes. 04/17/11 -- Added a 'WholeGenomeFasta' directory to the Sequence directory of each iGenomes. This new directory contains a single multi-fasta file with all chromosome sequences. The BowtieIndex directory now contains a symoblic link to this file. 04/17/11 -- Added a 'SmallRNA' directory to the Annotation directory of each iGenome. For species where data is available, microRNA sequence files of both mature and immature sequences will be added to the new directory. 04/17/11 -- Removed older GenomeStudio Archives of NCBI genomes since chromosome names no longer match new NCBI chromosome names. The files from these archives will still be available in the Annotation Archives directories. 04/17/11 -- Removed splice_sites directories from all current Annotation directories, since these were for deprecated CASAVA v1.6. 04/17/11 -- Updated NCBI genomes annotation files (to accomodate new chromosome names). 03/16/11 -- Added bacterial genome Sorangium_cellulosum_So_ce_56, source NCBI, build 2007-11-27. 03/16/11 -- Added yeast genome Schizosaccharomyces_pombe, source Ensembl, build EF1. 02/14/11 -- Updated external iGenomes (on iCom). 02/07/11 -- Changed directory structure of Annotation directory to contain subdirectories Gene, Variation, and Archives. The Archives directory now contains all archives as subdirectories (this also applies to the new GenomeStudio Archives directory). Due to this directory structure has change, PLEASE RE-DOWNLOAD ALL IGENOMES THAT WERE DOWNLOADED PRIOR TO THIS DATE. 02/07/11 -- Updated all iGenomes annotation files. 02/07/11 -- Added new species rice, sorghum, and corn (Ensembl release 7). 02/07/11 -- Added new bacterial 'species' B. cereus ATCC 10987, P. aeruginosa PAO1, R. sphaeroides 2.4.1, and S. aureus NCTC 8325 (NCBI). 02/07/11 -- Added new build UMD3.1 build of cow from NCBI. 02/07/11 -- Added new source for 'species' PhiX, source Illumina, build name RTA. This reference sequence is used by Illumina RTA software when calculating error rates. 02/07/11 -- Added variation annotation for Human for NCBI and UCSC. 02/07/11 -- Consolidated Ensembl builds such that the iGenome build name is the assembly name. The README.txt file in the Annotation directory now contains the Ensembl release number of the current annotation files. Information that was in VERSION.txt files is now included in the README.txt. 02/07/11 -- NCBI build names have been updated for cow, horse, pig, rat, and C. elegans. This update required naming cow Btau4.0 to Btau4.2, horse build2.1 to EquCab2.0, rat build4.1 to RGSC_v3.4, and C. elegans build8.1 to WS190. Pig build 1.1 was replaced with Sscrofa9.2. 02/07/11 -- Removed all NCBI seq_gene.md.gz files in favor of refFlat.txt.gz. All iGenomes with available annotation files should now have a refFlat.txt.gz and a GTF file. Previous custom refFlat files, such as refFlat.eland_rnav.17.txt.gz, are now simply named refFlat.txt and customizations are noted in the Annotation README.txt. 02/07/11 -- Removed kgXref.txt, knownToRefSeq.txt, refSeqSummary.txt, and cytoBand.txt annotation files from NCBI genomes. 02/07/11 -- Modified entry in human Ensembl refFlat.txt and refGene.txt, which caused an error in CASAVA v1.7: C17orf88 02/07/11 -- Renamed PhiX chromosome name to phix.fa (from chr.fa). 02/07/11 -- Removed splice sites directories from UCSC Annotation directories since CASAVA v1.6 only works with NCBI-style chromosome names. 02/07/11 -- The README.txt file in the Annotation directory now contains the date that annotation files were last downloaded. 01/28/11 -- Renamed refFlat.eland_rnav1.7.txt.gz to refFlat.txt.gz for Human UCSC and Ensembl, since AVC requires the exact name refFlat.txt.gz. 10/19/10 -- Changed the name of SquashedChromosomes directory to Squashed-species-source-build. This way, the species, source, and build will appear in GERALD's Summary.htm. 10/19/10 -- Added the iGenomes overview README.txt to the top-level of each compressed iGenome. 10/19/10 -- Gene coordinate annotation is missing from Cow and Rat from NCBI, since the seq_gene.md is currently absent from the NCBI ftp site. 10/19/10 -- Begin Change Log