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apolloh

Hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

bamdst

a lightweight bam file depth statistical tool

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

breakid

BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split read

canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

charger

Characterization of Germline variants

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

firebrowser

An R client for broads firehose pipeline, providing TCGA data sets

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

genefuse

Gene fusion detection and visualization

gsea-desktop

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

hla

xHLA: Fast and accurate HLA typing from short read sequence data

hotspot3d

3D hotspot mutation proximity analysis tool

htslib

C library for high-throughput sequencing data formats

isown

ldblockshow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

loftee

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

mixcr

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

msisensor

microsatellite instability detection using paired tumor-normal

muts-needle-plot

A needle plot for mutation data

neopredpipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

ngstools

Programs to analyse NGS data for population genetics purposes

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pipipes

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

seqtk

Toolkit for processing sequences in FASTA/Q formats

sgz