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Genomes and software

These are the genome indices and analysis software available via pysano. This page was last updated on March 5, 2015.


Genome indexes

Arabidopsis genome build At10

Novoalign indexes:
  • at10EnsTransRad46Num100kMin10SplicesChrPhiXAdaptrBuild22.nov.illumina.nix

C_elegans genome build Ce6

Novoalign indexes:
  • ce6EnsTrans97AdaptPhiFixed.nov.illumina.nix
  • ce6EnsTransRad97Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix

C_elegans genome build Ce10

Novoalign indexes:
  • ce10AdaptPhiX.nov.illumina.nix
  • ce10WBTransRad32Num100kMin10AdaptPhiX.nov.illumina.nix
  • ce10WBTransRad46Num100kMin10AdaptPhiX.nov.illumina.nix
  • ce10WBTransRad68Num100kMin10AdaptPhiX.nov.illumina.nix
  • ce10WBTransRad97Num100kMin10AdaptPhiX.nov.illumina.nix
Other files:
  • ce10.fasta
  • ce10.fasta.fai

Drosophila genome build Dm3

Novoalign indexes:
  • dm3.nov.illumina.nix
  • dm3EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • dm3PhiXAdaptr.nov.illumina.nix

Human genome build Hg38

Novoalign indexes:
  • hg38EnsGeneAdptrPhiX_chr16PlusChr16OddChroms.nov.illumina.nix
  • hg38RefSeqNoOddChroms.nov.illumina.nix
  • hg38RefSeqNoOddChromsChrLambPhiAdapt.nov.bisulphite.nix
  • hg38RefSeqNoOddChromsRad46Num100kMin10Splices.nov.illumina.nix
  • hg38RefSeqNoOddChromsRad97Num10kMin10Splices.nov.illumina.nix
Other files:
  • 0ReadMe.txt
  • Ensembl_GRCh38.76.genePredExt.gz
  • Ensembl_GRCh38.76.gtf.gz
  • Ensembl_GRCh38.76.refFlat.gz
  • Ensembl_GRCh38.76.refFlat_Merged.ucsc.gz
  • hg38EnsGene.ucsc.gz
  • hg38EnsGene_chr16.ucsc.gz
  • hg38RefGeneTableAllChroms.ucsc.gz
  • hg38RefGeneTableNoOddChroms.ucsc.gz

Human genome build Hg19

Novoalign indexes:
  • Hg19_masked_JP.nov.bisulphite.nix
  • Hg19_masked_agestudy.nov.bisulfite.nix
  • hg19.b.nix
  • hg19.nov.bisulphite.nix
  • hg19.nov.illumina.nix
  • hg19.nov.solid.nix
  • hg19AllChromsEbvDQ278827.nov.illumina.nix
  • hg19AllChromsKhsvGQ994935.nov.illumina.nix
  • hg19AllPhiXAdapt.nov.illumina.nix
  • hg19Axl.nov.illumina.nix
  • hg19C9orf127.nov.illumina.nix
  • hg19Chr19Rad96.nov.illumina.nix
  • hg19ChrMLambda.nov.bisulphite.nix
  • hg19ChromPlusRandomPhiXAdaptrStep1Kmer12.nov.illumina.nix
  • hg19EnsGeneRad46Num100kMin10Splices.nov.bisulphite.nix
  • hg19EnsGeneTableRad97Num10kMin10Splices.nov.bisulphite.nix
  • hg19EnsGeneTableRad97Num10kMin10Splices.nov.illumina.nix
  • hg19EnsGenesRad46Build74AdaptPhixChrUnAll.nov.bisulphite.nix
  • hg19EnsGenesRad46Build74AdaptPhixChrUnAll.nov.illumina.nix
  • hg19EnsGenesRad46Build74AdaptPhixChrUnAllRevCambChrM.nov.illumina.nix
  • hg19EnsTransBuild74D1279927Num100kMin10Splices.nov.illumina.nix
  • hg19EnsTransBuild74KC207813Num100kMin10Splices.nov.illumina.nix
  • hg19EnsTransBuild74Rad46.nov.illumina.nix
  • hg19EnsTransKnwnRad97Num10kMin10SplicesEBV.nov.illumina.nix
  • hg19EnsTransRad31Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • hg19EnsTransRad41Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • hg19EnsTransRad46Build74AdaptPhiX_SingleCellRNASpikes.nov.illumina.nix
  • hg19EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • hg19EnsTransRad46Num100kMin10SplicesChrPhiXAdaptrEBV.nov.illumina.nix
  • hg19EnsTransRad46Num100kMin10SplicesChrPhiXAdaptrKSHV.nov.illumina.nix
  • hg19EnsTransRad72Num100kMin10SplicesMarti.nov.illumina.nix
  • hg19FullDemian.nov.illumina.nix
  • hg19FullEbvDemian.nov.illumina.nix
  • hg19FullKSHVDemian.nov.illumina.nix
  • hg19GQ994935EnsTransRad46.nov.illumina.nix
  • hg19KnownTransRad46Num100kMin10Splices.nov.illumina.nix
  • hg19NormChrLambPhiAdapt.nov.bisulphite.nix
  • hg19NormPhiXAdapt.nov.illumina.nix
  • hg19PlusKHSV.nov.illumina.nix
  • hg19Ribo.nov.illumina.nix
  • hg19Survivin.nov.illumina.nix
  • hg19TransEnsKnwnRad97Num10kMin10.nov.illumina.nix
  • hg19_HumanAdenovirus_C-strain_USA_CL_42.nov.illumina.nix
  • hg19_v3.nov.illumina.nix
  • hg19cj3EnsTransRad46Num100kMin10SplicesChrPhiXAdaptrHVS.nov.illumina.nix
  • hg19hairpin.nov.illumina.nix
  • hg19htra1.nov.illumina.nix
  • hg19mask.nov.illumina.nix
Other files:
  • dbANNOVAR
  • hg19.1000G_EUR_0.05.indel.vcf
  • hg19.1000G_EUR_0.05.snp.vcf
  • hg19.1000G_biallelic.indels.intervals
  • hg19.1000G_omni2.5.g25.vcf
  • hg19.1000G_omni2.5.vcf
  • hg19.1000G_omni2.5.vcf.idx
  • hg19.1000G_phase1.indels.g25.vcf
  • hg19.1000G_phase1.indels.interval
  • hg19.1000G_phase1.indels.vcf
  • hg19.1000G_phase1.indels.vcf.idx
  • hg19.1000G_phase1.snps.high_confidence.g25.vcf
  • hg19.1000G_phase1.snps.high_confidence.vcf
  • hg19.Mills_and_1000G_gold_standard.indels.g25.vcf
  • hg19.Mills_and_1000G_gold_standard.indels.vcf
  • hg19.Mills_and_1000G_gold_standard.indels.vcf.idx
  • hg19.b.dict
  • hg19.b.fa
  • hg19.b.fa.dict
  • hg19.b.fa.fai
  • hg19.bwa.illumina.amb
  • hg19.bwa.illumina.ann
  • hg19.bwa.illumina.bwt
  • hg19.bwa.illumina.pac
  • hg19.bwa.illumina.sa
  • hg19.bwa.solid.amb
  • hg19.bwa.solid.ann
  • hg19.bwa.solid.bwt
  • hg19.bwa.solid.nt.amb
  • hg19.bwa.solid.nt.ann
  • hg19.bwa.solid.nt.pac
  • hg19.bwa.solid.pac
  • hg19.bwa.solid.sa
  • hg19.chr1.dict
  • hg19.chr1.fasta
  • hg19.chr1.fasta.fai
  • hg19.chr2.dict
  • hg19.chr2.fasta
  • hg19.chr2.fasta.fai
  • hg19.chr3.dict
  • hg19.chr3.fasta
  • hg19.chr3.fasta.fai
  • hg19.dbsnp.vcf
  • hg19.dbsnp.vcf.idx
  • hg19.dbsnp_132.vcf
  • hg19.dbsnp_132.vcf.idx
  • hg19.dbsnp_137.excluding_sites_after_129.g25.vcf
  • hg19.dbsnp_137.excluding_sites_after_129.vcf
  • hg19.dbsnp_137.g25.vcf
  • hg19.dbsnp_137.vcf
  • hg19.dict
  • hg19.ensgenes.ucsc
  • hg19.ensproteincodinggenes.ucsc
  • hg19.fasta
  • hg19.fasta.fai
  • hg19.hapmap_3.3.g25.vcf
  • hg19.hapmap_3.3.vcf
  • hg19.hapmap_3.3.vcf.idx
  • hg19.indel.intervals
  • hg19.refgene.gff3
  • hg19.refgene.vgi
  • hg19.ucscgene.knowngene.txt
  • hg19.vfi
  • hg19AllPhiXAdapt.nov.illumina.nix.bldNotes.txt
  • hg19EnsGenesMergedNoOverlap.txt
  • hg19EnsGenesNoOddChromsEBV.ucsc
  • hg19EnsGenesNoOddChromsKSHV.ucsc
  • hg19EnsGenesWithNames.refflat.ucsc
  • hg19StandardChrUnAll.dict
  • hg19StandardChrUnAll.fasta
  • hg19StandardChrUnAll.fasta.fai
  • hg19_ALL.sites.2010_11.txt
  • hg19_ALL.sites.2010_11.txt.idx
  • hg19_avsift.txt
  • hg19_avsift.txt.idx
  • hg19_ensGene.txt
  • hg19_ensGeneMrna.fa
  • hg19_genomicSuperDups.txt
  • hg19_kgXref.txt
  • hg19_knownGene.txt
  • hg19_knownGeneMrna.fa
  • hg19_ljb_lrt.txt
  • hg19_ljb_mt.txt
  • hg19_ljb_phylop.txt
  • hg19_ljb_pp2.txt
  • hg19_phastConsElements46way.txt
  • hg19_refGene.txt
  • hg19_refGeneMrna.fa
  • hg19_refLink.txt
  • hg19_snp132.txt
  • hg19_snp137.txt
  • hg19_snp137.txt.idx

Human genome build Hg18

Novoalign indexes:
  • hg18.nov.illumina.nix
  • hg18EnsTransRad32Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • hg18EnsTransRad39Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • hg18NormChrLambPhiAdapt.nov.bisulphite.nix
  • hg18UCSCRefFlatRad46Num100kMin10SplicesAdaperPhiX.nov.illumina.nix
Other files:
  • hg18.ensprotcodinggenes.ucsc
  • hg18.fasta

Human genome build B37

Novoalign indexes:
  • human_g1k_v37_decoy_phiXAdaptr.nov.illumina.nix
  • human_g1k_v37_phiXAdaptr.nov.illumina.nix
Other files:
  • 1000G_omni2.5.b37.vcf
  • 1000G_omni2.5.b37.vcf.idx
  • 1000G_phase1.indels.b37.vcf
  • 1000G_phase1.indels.b37.vcf.idx
  • 1000G_phase1.snps.high_confidence.b37.vcf
  • 1000G_phase1.snps.high_confidence.b37.vcf.idx
  • 2.8
  • Mills_and_1000G_gold_standard.indels.b37.vcf
  • Mills_and_1000G_gold_standard.indels.b37.vcf.idx
  • MuTect
  • SureSelect
  • chrPhiX_Illumina.fasta
  • dbsnp_137.b37.excluding_sites_after_129.vcf
  • dbsnp_137.b37.excluding_sites_after_129.vcf.idx
  • dbsnp_137.b37.vcf
  • dbsnp_137.b37.vcf.idx
  • hapmap_3.3.b37.vcf
  • hapmap_3.3.b37.vcf.idx
  • hg19.ccds.20131019.bed
  • hs37d5.dict
  • hs37d5.fa
  • hs37d5.fa.fai
  • hs37d5_simple.dict
  • hs37d5_simple.fa
  • hs37d5_simple.fa.fai
  • human_g1k_v37.dict
  • human_g1k_v37.fasta
  • human_g1k_v37.fasta.fai
  • human_g1k_v37_decoy.dict
  • human_g1k_v37_decoy.fasta
  • human_g1k_v37_decoy.fasta.fai
  • human_g1k_v37_decoy.vfi
  • human_g1k_v37_decoy_phiXAdaptr.dict
  • human_g1k_v37_decoy_phiXAdaptr.fasta
  • human_g1k_v37_decoy_phiXAdaptr.fasta.amb
  • human_g1k_v37_decoy_phiXAdaptr.fasta.ann
  • human_g1k_v37_decoy_phiXAdaptr.fasta.bwt
  • human_g1k_v37_decoy_phiXAdaptr.fasta.fai
  • human_g1k_v37_decoy_phiXAdaptr.fasta.pac
  • human_g1k_v37_decoy_phiXAdaptr.fasta.sa
  • human_g1k_v37_phiXAdaptr.fasta
  • human_g1k_v37_phiXAdaptr.fasta.amb
  • human_g1k_v37_phiXAdaptr.fasta.ann
  • human_g1k_v37_phiXAdaptr.fasta.bwt
  • human_g1k_v37_phiXAdaptr.fasta.fai
  • human_g1k_v37_phiXAdaptr.fasta.pac
  • human_g1k_v37_phiXAdaptr.fasta.sa

M_fascicularis genome build Mf5

Novoalign indexes:
  • mf5.0v3rad97Num20kMin1010136X2_10136X8iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin1010136X3_10136X9iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin1010136X5_10136X8iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10136X6_10136X11iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10136X6_10479X4iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10479X1_10136X7iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10479X2_10136X7iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10479X3_10136X10iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10_10136x1_10136x7iupac.nov.illumina.nix
  • mf5.0v3rad97Num20kMin10_10136x4_10136x10iupac.nov.illumina.nix

Marmoset genome build Cj3

Novoalign indexes:
  • cj3EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • cj3EnsTransRad46Num100kMin10SplicesChrPhiXAdaptrHVS.nov.illumina.nix
  • cj3HVSDemian.nov.illumina.nix
Other files:
  • cj3EnsGenesStandard.ucsc
  • cj3EnsGenesStandardHSV.ucsc

Mouse genome build Mm9

Novoalign indexes:
  • mm9.nov.bisulphite.nix
  • mm9.nov.illumina.nix
  • mm9.nov.solid.nix
  • mm9EnsTransRad32Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • mm9EnsTransRad39Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • mm9EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • mm9EnsTransRad56Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • mm9EnsTransRad97Num10kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • mm9EnsTransRad97Num10kMin10SplicesChrPhiXAdaptrLambda.nov.bisulphite.nix
  • mm9NormChromAdaptLambPhi.nov.bisulphite.nix
  • mm9NormChromAdaptLambPhi.nov.illumina.nix
  • mm9VK-BS-UcscEnsSplice90_k13_s3.nov.bisulphite.nix
  • mm9VK-NBS-UcscEnsSplice90_k13_s3.nov.illumina.nix
  • mm9splices34.nov.illumina.nix
Other files:
  • mm9.dbsnp_132.vcf
  • mm9.dbsnp_132.vcf.idx
  • mm9.dict
  • mm9.ensgene.txt
  • mm9.ensgenes.ucsc
  • mm9.fasta
  • mm9.fasta.fai
  • mm9.ucscgene.knowngene.exon.bed
  • mm9.ucscgene.knowngene.txt
  • mm9EnsGenes_NoOverlappingExons.txt

Mouse genome build Mm10

Novoalign indexes:
  • mm10.nov.illumina.nix
  • mm10EnsGenesRad97PhixAdapter.nov3.bisulfite.nix
  • mm10EnsGenesRad97PhixAdapter.nov3.illumina.nix
  • mm10EnsRad97Num10kMin10Splices.nov.illumina.nix
  • mm10EnsTrans46bpNum100kMin10SplicesChrNormPhiXAdaptrEns74.nov.illumina.nix
  • mm10EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr_separateHumanMouseAtxn2.nov.illumina.nix
  • mm10EnsTransRad46bpNum100kMin10SplicesChrNormPhiXAdaptr.nov.illumina.nix
  • mm10EnsTransRad97Num100Min10SplicesChrPhiXAdaptr1.nov.illumina.nix
  • mm10EnsTransRad97Num100Min10SplicesChrPhiXAdaptr2.nov.illumina.nix
Other files:
  • mm10.fasta
  • mm10.fasta.fai
  • mm10.standard.dict
  • mm10.standard.fasta
  • mm10.standard.fasta.fai
  • mm10.ucsc.PSC.xls
  • mm10.ucsc.txt
  • mm10EnsGene.NoOddChroms.PSC.ucsc
  • mm10EnsGene.NoOddChroms.PSC_Merged.ucsc
  • mm10EnsGene.PSC.ucsc
  • mm10EnsGenes20130930.txt
  • rename

Rat genome build Rn5

Novoalign indexes:
  • rn5EnsTransRad46Build75ChrPhiXAdaptr.nov.illumina.nix
  • rn5RefSeqTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix

Rat genome build Rn4

Novoalign indexes:
  • rn4.nov.illumina.nix
  • rn4EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
Other files:
  • rn4.bwa.illumina.amb
  • rn4.bwa.illumina.ann
  • rn4.bwa.illumina.bwt
  • rn4.bwa.illumina.pac
  • rn4.bwa.illumina.sa
  • rn4.dict
  • rn4.fasta
  • rn4.fasta.fai

S_cerevisiae genome build Sc3

Novoalign indexes:
  • Sc3.EnsemblRad121PhixAdapter.nov3.bisulfite.nix
  • Sc3.EnsemblRad121PhixAdapter.nov3.illumina.nix
  • Sc3.SacCer3.nov.illumina.nix
  • Sc3.SacCer3_wSplices_Rad30.nov.illumina.nix

Zebrafish genome build Zv9

Novoalign indexes:
  • danRer7_masked.nov.illumina.nix
  • zv9AllChrLambPhiAdapt.nov.bisulphite.nix
  • zv9AllStdChrLambPhiAdaptr.nov.bisulphite.nix
  • zv9AllStdChrLambPhiAdaptr.nov.illumina.nix
  • zv9ContigScaffold.nov.illumina.nix
  • zv9EnsTransRad121Num10kMin10SplicesChrPhiXAdaptrNoOddChroms.01-13-15.nov.illumina.nix
  • zv9EnsTransRad32Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • zv9EnsTransRad32Num100kMin10SplicesChrPhiXAdaptr2.nov.illumina.nix
  • zv9EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.illumina.nix
  • zv9EnsTransRad46Num100kMin10SplicesChrPhiXAdaptr.nov.solid.nix
  • zv9EnsTransRad46Num100kMin10SplicesChrPhiXAdaptrRNASpikes_eGFP_mCherry.01-09-15.nov.illumina.nix
  • zv9EnsTransRad46Num100kMin10SplicesPhiXAdaptr201305.nov.illumina.nix
  • zv9_contig_phix_adapter_lambda.nov.illumina.nix
  • zv9spikein.nov.illumina.nix
Other files:
  • danRer7_masked.fa
  • danRer7_masked.fa.fai
  • zv9.ensemblgenes.ucsc
  • zv9.ensemblgenes.ucsc.fai
  • zv9.ensembltranscripts.ucsc
  • zv9AllChrLambPhiAdapt.nov.bisulphite.nix.fai
  • zv9ContigScaffold.bwa.illumina.amb
  • zv9ContigScaffold.bwa.illumina.ann
  • zv9ContigScaffold.bwa.illumina.bwt
  • zv9ContigScaffold.bwa.illumina.pac
  • zv9ContigScaffold.bwa.illumina.sa
  • zv9EnsGene_01-07-2015.mCherryEGFP_RNA_Spikes.ucsc.gz
  • zv9EnsGene_01-07-2015.mCherryEGFP_RNA_Spikes_Merged.ucsc.gz
  • zv9EnsTrans201305.txt
  • zv9EnsTrans201305_Merged.ucsc

Zebrafish genome build Zv10

Novoalign indexes:
  • zv10AllStdChrPhiAdapt.nov.illumina.nix
  • zv10NCBIRefSeqAllStdChrRad46Num10kMin10Splices.nov.illumina.nix
Other files:
  • 0ReadMe.txt
  • zv10AllStdChrPhiAdapt.tar.gz
  • zv10NCBIRefSeq_Rad46Num10kMin10Splices.fasta.gz
  • zv10_NCBIRefSeq.ucsc
  • zv10_NCBIRefSeq_Merged.ucsc

Analysis Software

By default, pysano will use the most recent version of any program you specify. If you need an older version you must use its full path name.

  • annovar version 20141114 (also 2012May25, 01.22.2013, 0.1 )
  • bedtools version 2.22.1 (also 2.16.2 )
  • bwa version 0.7.8 (also 0.7.5, 0.6.2 )
  • ccmdoc version 2.07
  • clint version 1.0
  • contSeqs version zooBWAdb
  • ExaBayes version 1.4.1
  • FastQC version 0.10.1
  • Fastx-toolkit version 0.0.13
  • gatk version 3.3-2 (also 3.3-0, 3.2-2, 3.1-1, 2.7-2, 2.4-9, 2.4-7, 2.4-3, 2.3-9, 2.3-0 )
  • igv version 2.1.25
  • IGVTools version 2.3.68
  • java version jre1.7.0_40 (also jre1.6.0_45 )
  • misc version 0.1
  • MuTect version 1.1.4
  • novoalign version 3.02.07 (also 3.00.02, 2.08.03, 2.08.01 )
  • novoalignCS version 1.02.1
  • picard version 1.119  (also 1.84, 1.75, 1.87, 1.112, 1.100 )
  • r version 3.0.3
  • samblaster version 0.1.21
  • samtools version 1.0 (also 0.1.19, 0.1.18-dev )
  • scythe version 0.981
  • sickle version 1.200
  • snpEff version 3.0
  • SomaticSniper version 1.0.4
  • sratoolkit version 2.1.16
  • Strelka version 1.0.14
  • tabix version 0.2.6 (also 0.2.5 )
  • UCSC version wigToBigWig (also bigWigToWig, bigWigToBedGraph, bigWigInfo, bigBedToBed, bigBedInfo, bedToBigBed, bedGraphToBigWig, bedClip )
  • useq version 8.8.8 (also 8.8.1, 8.8.0, 8.7.8, 8.7.4, 8.7.1, 8.6.6, 8.5.0, 8.3.9 )
  • VAAST version 2.1.0 (also 1.0.4, 1.0.0 )
  • VarScan version 2.3.7 (also 2.3.5 )
  • vcftools version 0.1.11