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hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

htslib

C library for high-throughput sequencing data formats

iannotatesv

iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data.

icallsv

A Framework to call Structural Variants from NGS based datasets

impact-pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

jvarkit

Java utilities for Bioinformatics

lancet

Microassembly based somatic variant caller for NGS data

learn-bioinformatics

List of resources for learning bioinformatics, from beginner to advanced

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

mageri

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

mageri-paper

Data and post-analysis for MAGERI project

mirmmr

Microsatellite Instability Regression using Methylation and Mutations in R

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.

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

mutalyzer

HGVS variant nomenclature checker

mutation-mapper

mutation_analysis_scripts

day to day activity for mutation data

ngs

PennSCAP-T Pipeline

ngs-1

Python wrappers for common NGS tools used by the Bioinformatics Core team at the Princess Margaret Cancer Centre

ngs-2

my python code.

ngs-3

Scripts for next generation sequencing

ngs-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology

ngs-pipeline

NGS pipeline based on the python module ruffus

ngscheckmate

Software program for checking sample matching for NGS data

ngsclean-1

Pipeline for NGS read (filtering, trimming, merging) and SNP (quality, depth, biases, ...) quality control

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

ngstools

Next-Generation Sequencing(NGS) toolkits.

ngsutils

Tools for next-generation sequencing analysis