nh13

DWGSIM

Whole Genome Simulator for Next-Generation Sequencing

samtools

callerpp

A simple consensus caller based on partial order alignment with spoa

ksw

Ksw: (interactive) smith-waterman in C

MultiQC

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

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

seq_io

FASTA and FASTQ parsing in Rust

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

bioconda-recipes

Conda recipes for the bioconda channel.

biopython

Official git repository for Biopython (originally converted from CVS)

cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

conda-env-builder-feedstock

A conda-smithy repository for conda-env-builder.

fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

latch

a python bioinformatics framework

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

nextflow

A DSL for data-driven computational pipelines

nf-co.re

Code and files for the main nf-core website.

pizzly

Fast fusion detection using kallisto

pLannotate

Webserver and command line tool for annotating engineered plasmids

prometheus-feedstock

A conda-smithy repository for prometheus.

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

rust-bio-types

A library of common biomedical types.

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

rust-pseudoaligner

Single-Cell RNA-seq pseudo-aligner

slippy

Simple Snakemake Linter

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

stitch

Alignment for vector quality control

SystematicDiscoveryRecombinases2022

Additional data and code to accompany the publication: "Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome." 2022, Nature Biotechnology.

test-datasets

Test data to be used for automated testing with the nf-core pipelines

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms