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