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10x-manipulation-tools

Some internal tools for manipulating FASTQ and BAM files with barcoded short reads

acc2tax

Tool for quick offline batch conversion of Genbank IDs or accessions to taxonomy strings

aegean

Integrated toolkit for analysis and evaluation of annotated genomes

amplici

AmpliCI, a model-based algorithm for denoising Illumina amplicon data.

amplici-umi

AmpliCI with UMI information

ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

ape

A Plasmid Editor

atlas-utils

tools for microbiome data analysis

badaboum

BAdabouM is a genomic structural variations discovery tool

bam2fastq

Simple convertor from bam to FASTQ

bamcov

:boom: Quickly calculate and visualize sequence coverage in alignment files

bash-oneliner

A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.

bash-oo-framework

Bash Infinity is a modern boilerplate / framework / standard library for bash

bcbio_validation_workflows

A community menagarie of automated variant validations using bcbio and the Common Workflow Language

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

bcfanno

A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file

bedd

tiny yet fully functional text editor for linux, with mouse support and more!

bgtf

In-memory/on-disk storage and random accession of GTF file

bioinformatics_primer

Bioinformatics with Unix, bash, Make, Python, and parallel

bloom

Bloom filter implementation

boogiesync-tablet

A userspace linux driver (written in C using libevdev and libbluetooth) for using the Boogie Board Sync 9.7 as a tablet input device

book

bri

Bam Read Index - Extract alignments from a bam file by readname

c

Collection of various algorithms in mathematics, machine learning, computer science, physics, etc implemented in C for educational purposes.

cbio

cBio is a free Open Source extended software analysis library and package originally based on EMBOSS

cfdnapipe

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

cgranges

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

cheatsheets

My cheatsheets

cloneit

github repo for Bioinformatics. 1998 Jun;14(5):465-6. CloneIt: finding cloning strategies, in-frame deletions and frameshifts.

cmph

C Minimal Perfect Hashing Library