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argparse_dataclass

Declarative CLIs with argparse and dataclasses

augur

Pipeline components for real-time phylodynamic analysis

aws-elastic-beanstalk-cli

The EB CLI is a command line interface for Elastic Beanstalk that provides interactive commands that simplify creating, updating and monitoring environments from a local repository.

bayesianmethods

biod

Bioinformatics library in D. (utils for working with SAM, BAM, SFF formats)

bwa-mem2

The next version of bwa-mem (WIP; not recommended for production uses at the moment)

canu

A single molecule sequence assembler for genomes large and small.

cas-offinder

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

cdna-display-proteolysis-pipeline

cpython

The Python programming language

dna-me-pipeline

DCC/DAC methylation pipeline source

dnachisel

:pencil2: A versatile DNA sequence optimizer

dnanexus

editdistance

Fast implementation of the edit distance(Levenshtein distance)

falcon

FALCON: experimental PacBio diploid assembler

falcon-integrate

Build and integration- testing for FALCON

fastq_compression_comparison

Creating a simple Docker image to help perform comparisons for FASTQ compression

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

hi-c-scaffold

SALSA: A tool to scaffold long read assemblies with Hi-C data

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

learning-jenkins-3003221

Learning Jenkins

mash

Fast genome and metagenome distance estimation using MinHash

mohrs_circle

Example Streamlit code for Mohrs Circle

mslib

MSL is a C++ library that enables the computational study of macromolecules.

parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

platypus

Platypus Variant Caller

pre-commit

A collection of pre-commit hooks used by Gruntwork tools

pybgen

Python module to process BGEN files as dosage data

pycoqc

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

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.