common_analyses

Repository of common bioinformatics scripts. Below are the contents and a short description of what it does.

Running GATK program

Scripts required

GATK_00_PrepareRef.sh
GATK_01_RunBWA.sh
GATK_02_DataCleanup.sh
GATK_03_BaseRecalibrator.sh
GATK_04_combinedRun.sh
GATK_05_FilterSNP.sh

Running de novo transcript assembly and getting counts for calculating DGE

RSEM_01_trinity.sh
RSEM_02_estm.sh
RSEM_03_dge.sh
runTrinity.sh

Gene Prediction Training related

runAugustus.sh
runTraining.sh
runBraker.sh

VCF files related

runBEAGLE_PhaseImpute.sh
runVCFstats.sh
runTASSEL_GBSv2.sh
runTasselGWAS.sh
runBayesScan.sh
runSTRUCTURE.sh

Genome Assembly

runMaSuRCA.sh
rundipSPAdes.sh
runPlatanus.sh
runSOAP.sh
runSPAdes.sh

Alignment

runHISAT2.sh
runSTAR.sh
runBWAcrossspp.sh
runBlasr.sh

BLAST

runBLASTn.sh
runBLASTp.sh
runBLASTx.sh
runMegablast.sh

Assembly processing

runBlobtools.sh
runBUSCO.sh
runCEGMA.sh
runDigiNorm_pe.sh
runGenomeScope.sh
runKHMER.sh
runSynteny.sh
runRepeatModeler.sh

Phylogenetics

runGuidenceAA.sh
runGuidenceNT.sh
runRAxML.sh

General purpose

runFASTQC.sh

Name		Name	Last commit message	Last commit date
Latest commit History 134 Commits
BlastXMLmerge.py		BlastXMLmerge.py
GATK_00_PrepareRef.sh		GATK_00_PrepareRef.sh
GATK_01_RunBWA.sh		GATK_01_RunBWA.sh
GATK_02_DataCleanup.sh		GATK_02_DataCleanup.sh
GATK_03_BaseRecalibrator.sh		GATK_03_BaseRecalibrator.sh
GATK_04_combinedRun.sh		GATK_04_combinedRun.sh
GATK_05_FilterSNP.sh		GATK_05_FilterSNP.sh
GetBaseSpace.sh		GetBaseSpace.sh
README.md		README.md
RSEM_01_trinity.sh		RSEM_01_trinity.sh
RSEM_02_estm.sh		RSEM_02_estm.sh
RSEM_03_dge.sh		RSEM_03_dge.sh
agp2fasta.pl		agp2fasta.pl
agp_validate		agp_validate
generate_i-AdHore_ini-file.sh		generate_i-AdHore_ini-file.sh
pafCoordsDotPlotly.R		pafCoordsDotPlotly.R
runAbyss.sh		runAbyss.sh
runAlignmentStats.sh		runAlignmentStats.sh
runAugustus.sh		runAugustus.sh
runBEAGLE_PhaseImpute.sh		runBEAGLE_PhaseImpute.sh
runBLASTn.sh		runBLASTn.sh
runBLASTp.sh		runBLASTp.sh
runBLASTx.sh		runBLASTx.sh
runBUSCO.sh		runBUSCO.sh
runBWA.sh		runBWA.sh
runBWAcrossspp.sh		runBWAcrossspp.sh
runBayesScan.sh		runBayesScan.sh
runBlasr.sh		runBlasr.sh
runBlobtools.sh		runBlobtools.sh
runBowtie2.sh		runBowtie2.sh
runBraker.sh		runBraker.sh
runCEGMA.sh		runCEGMA.sh
runClass2.sh		runClass2.sh
runCufflinks.sh		runCufflinks.sh
runDigiNorm_pe.sh		runDigiNorm_pe.sh
runFASTQC.sh		runFASTQC.sh
runGMAP.sh		runGMAP.sh
runGSNAP.sh		runGSNAP.sh
runGenomeScope.sh		runGenomeScope.sh
runGuidanceAA.sh		runGuidanceAA.sh
runGuidanceNT.sh		runGuidanceNT.sh
runHISAT2.sh		runHISAT2.sh
runHisat2.sh		runHisat2.sh
runKHMER.sh		runKHMER.sh
runMaSuRCA.sh		runMaSuRCA.sh
runMegablast.sh		runMegablast.sh
runOASES.sh		runOASES.sh
runPlatanus.sh		runPlatanus.sh
runRAxML.sh		runRAxML.sh
runRedundans.sh		runRedundans.sh
runRepeatModeler.sh		runRepeatModeler.sh
runSMRTccs.sh		runSMRTccs.sh
runSOAP.sh		runSOAP.sh
runSOAPtrans.sh		runSOAPtrans.sh
runSPAdes.sh		runSPAdes.sh
runSTAR.sh		runSTAR.sh
runSTARmap_index.sh		runSTARmap_index.sh
runSTARmap_round1.sh		runSTARmap_round1.sh
runSTARmap_round2.sh		runSTARmap_round2.sh
runSTRUCTURE.sh		runSTRUCTURE.sh
runSentieon_step2.sh		runSentieon_step2.sh
runSention_step1.sh		runSention_step1.sh
runStringtie.sh		runStringtie.sh
runSynteny.sh		runSynteny.sh
runTASSEL_GBSv2.sh		runTASSEL_GBSv2.sh
runTasselGWAS.sh		runTasselGWAS.sh
runTraining.sh		runTraining.sh
runTrinityGG.sh		runTrinityGG.sh
runTrinitySE.sh		runTrinitySE.sh
runVCFstats.sh		runVCFstats.sh
rundipSPAdes.sh		rundipSPAdes.sh
sjCollapseSamples.awk		sjCollapseSamples.awk
vcf-quality-distribution_p1.sh		vcf-quality-distribution_p1.sh
vcf-quality-distribution_p2.R		vcf-quality-distribution_p2.R

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