Common software packages

Pardon the dust

work in progress. check back later for a table of most commonly used software packages and their location in GHPC cluster.

DMU - http://www.dmu.agrsci.dk ADAM - http://adam.agrsci.dk/index.htm EVA - http://www.eva.agrsci.dk Bayz - http://bayz.biz/index.php?sc=11 Plink 1.9 http://zzz.bwh.harvard.edu/plink/plink2.shtml Beagle 5 https://faculty.washington.edu/browning/beagle/beagle_5.0_07Sep18.pdf (this is a moving target!) Bwa http://bio-bwa.sourceforge.net/bwa.shtml Samtools, bcftools, tabix http://www.htslib.org/doc/ GATK https://software.broadinstitute.org/gatk/documentation/ Picard https://broadinstitute.github.io/picard/command-line-overview.html NCBI-Blast https://www.ncbi.nlm.nih.gov/books/NBK279690/ (quite unreadable) SRA-Toolkit https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc Bamtools https://github.com/pezmaster31/bamtools/wiki/Tutorial_Toolkit_BamTools-1.0.pdf BamUtil https://genome.sph.umich.edu/wiki/BamUtil Trimmomatic http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf Vt https://genome.sph.umich.edu/wiki/Vt FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ Vcflib https://github.com/vcflib/vcflib Vcftools https://vcftools.github.io/man_latest.html Minimac4 https://genome.sph.umich.edu/wiki/Minimac4 VEP http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html Cutadapt https://cutadapt.readthedocs.io/en/stable/