kjl8

bioawk

BWK awk modified for biological data

RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.

tigra-sv

mTEA

Mosquito TE Annotation

snipper

A program for quickly researching genes and other genomic features near disease-associated regions of the genome (from GWAS or sequencing studies.)

somatic-sniper

A tool to call somatic single nucleotide variants.

Spanner

joinx

a tool for processing .bed and .vcf files

GWASViewer

Composite of Dygrap for GWAS and GeneViewer for Genes

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.

MOSAIK

reference-guided aligner for next-generation sequencing technologies

pmGWAS

perl modules for genome wide association studies

breakdancer

SV detection from paired end reads mapping