Fan-yuan

CancerVar

Clinical interpretation of somatic mutations in cancer

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

stranger

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

ExpansionHunter

A tool for estimating repeat sizes

str-analysis

Scripts and utilities related to analyzing short tandem repeats (STRs).

tredparse

TREDPARSE: HLI Short Tandem Repeat (STR) caller

ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences

ngs-bits

Short-read sequencing tools

seGMM

A new tool to infer sex from massively parallel sequencing data.

XYalign

Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data

XYalign

mummer

Mummer alignment tool

RedDog

sciclone

An R package for inferring the subclonal architecture of tumors

citup

Clonality inference in multiple tumor samples using phylogeny

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.

pyclone-vi

Fast method for inferring cancer clonal population structure from SNV data.

Create_PyClone_input

Python code to transform Sequenza segment output into PyClone input

DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

AmpSeq

A framework for semi-automated analysis of Amplicon Sequencing data

Canary

A fast and self-contained amplicon pipeline tool.

NGTAS_pipeline

Computational pipeline to analyse Next Generation Targeted Amplicon Sequence data

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.

ScanITD

A python tool to detect internal tandem duplication with robust variant allele frequency estimation

Genomon-ITDetector

for detecting internal tandem duplication from genome sequence data.

ITDetect

XCNV