compbio/ngseasy-full_no_gatk-gentoo repository overview

Allows execution of the full_no_gatk script contained within ngseasy or the ekg alignment and variant calling tutorial ( https://github.com/ekg/alignment-and-variant-calling-tutorial⁠ ).

Contains the following tools:

bioperl-1.6.9

goby-cpp-2.0.1

gmap-2012.07.20

htslib-1.1

lua-5.1.5-r3

bcftools-1.1

samtools-1.1

bedtools-2.20.1

vcflib-20141212

sambamba-0.5.1

samblaster-0.1.21

libStatGen-1.0.12

bamUtil-1.0.12

picard-1.103

fastqc-0.11.2-r1

trimmomatic-0.32

bamtools-2.3.0

freebayes-9.9.13

gatk-protected-3.3

seqtk-1.0

stampy-1.0.23

bwa-0.7.12

delly-0.6.1

lumpy-0.2.9

ExomeDepth-1.0.7

vcftools-0.1.12b