andreas-wilm

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ImmunoScape

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https://andreas-wilm.github.io/

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Andreas Wilm's starred repositories

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

sds

Simple Dynamic Strings library for C

Language:CBSD-2-Clause4861 142 41

clib

Package manager for the C programming language.

Language:CMIT4807 130 161

klib

A standalone and lightweight C library

Language:CMIT4095 193 100

uthash

C macros for hash tables and more

Language:CNOASSERTION4038 132 115

zlog

A reliable, high-performance, thread safe, flexsible, clear-model, pure C logging library.

Language:CApache-2.02146 134 186

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

Language:CNOASSERTION1589 102 1251

htslib

C library for high-throughput sequencing data formats

Language:CNOASSERTION789 64 703

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.

Language:CythonMIT769 48 915

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

Language:PythonBSD-2-Clause722 36 471

reviews

Writing reviews of academic papers

GPL-2.0464 36 3

pyfaidx

Efficient pythonic random access to fasta subsequences

Language:PythonNOASSERTION448 9 144

PyVCF

A Variant Call Format reader for Python.

Language:PythonNOASSERTION397 31 204

graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Language:C++MIT178 27 97

SeqPrep

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

Language:CMIT139 18 38

lofreq

LoFreq Star: Sensitive variant calling from sequencing data

Language:CNOASSERTION98 10 132

simplesam

Simple pure Python SAM parser and objects for working with SAM records

Language:PythonMIT61 7 17

libcfu

Updates to libcfu, orignally found here: http://libcfu.sourceforge.net/

Language:CNOASSERTION24 6 1

compbio-utils

miscellaneous bioinfo scripts

Language:Python8 30

consensus_from_mpileup

Scripts to compute simple consensus (SNPs, insertions, deletions) from mpileup by majority vote.

Language:Python4 2 2

my-dot-emacs

My .emacs file

Language:Common Lisp100

scif

Computes the SCI of an RNA alignment.

100