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assignment

bassovac

Improved Bayesian inversion somatic caller

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

breakdancer

SV detection from paired end reads mapping

cdhit

Automatically exported from code.google.com/p/cdhit

delly

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

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

hello-world

hotnet

HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.

lichee

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

multi-dendrix

my-first-repo

my-second-repo

paradigm-scripts

phylosub

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

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.

program

Bassovac

sciclone

An R package for inferring the subclonal architecture of tumors

somatic-sniper

A tool to call somatic single nucleotide variants.

sra-tools

SRA Tools

sratoolkit

SRAToolkit has been REPLACED - see README

the-unix-workbench

:house_with_garden: A Book for Anyone to Get Started with Unix

theta

Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.

tiedie

Tied Diffusion for Subnetwork Discovery (TieDIE)