madsheilskov's Stars
maxanes/Feature-Extraction-Workflow-for-Target-Mutation-Selection
Bioinformatics pipeline for the extraction of all tumor features necessary for selection of clonal mutations from whole-exome sequencing (WES) data in tumor normal settings
MOMA-CRC/ddanalyzor
Analysis of ddPCR raw data
adamewing/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
genome/bam-readcount
Count bases in BAM/CRAM files
Hogfeldt/ctDNAtool
A software for creating and manipulating statistics from cfDNA data
pysam-developers/pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
pughlab/ConsensusCruncher
ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.
msiemens/tinydb
TinyDB is a lightweight document oriented database optimized for your happiness :)
gerstung-lab/deepSNV
The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.
fulcrumgenomics/fgbio
Tools for working with genomic and high throughput sequencing data.
gwforg/gwf
A flexible, pragmatic workflow tool.
Gromgorgel/ddPCR
Digital PCR Analysis Algorithms
crazyhottommy/bioinformatics-one-liners
Bioinformatics one liners from Ming Tang
mailund/ctib
Lecture notes and material for Computational Thinking in Bioinformatics
nathan-russell/hashmap
Faster hash maps in R
eddelbuettel/littler
A scripting and command-line front-end for GNU R
docopt/docopt.R
Command-line interface description language for R (http://docopt.org)
alimanfoo/pysamstats
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
dkoboldt/varscan
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
NickSto/dunovo
WARNING: this repo is no longer updated. Main development has moved to:
OpenGene/AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
CGATOxford/UMI-tools
Tools for handling Unique Molecular Identifiers in NGS data sets
ARUP-NGS/BMFtools
Barcoded Molecular Families
galaxyproject/dunovo
Reference-free duplex sequencing pipeline.
xuchang116/smCounter
smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller", BMC Genomics, 2017 18:5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3425-4
GalliumOS/galliumos-distro
Docs, issues, and artwork sources for GalliumOS
libnano/primer3-py
Simple oligo analysis and primer design
quwubin/MFEprimer-2.0
MFEprimer-2.0: A fast thermodynamics-based program for checking PCR primer specificity
GTseq/GTseq-Pipeline
A series of perl and python scripts for generating genotypes from NGS fastq files from GTseq library sequencing.
Kennedy-Lab-UW/Duplex-Sequencing