donluistovar

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

NxTrim

Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.

AdapterRemoval

This program was developed to remove residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data.

metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS

fasta_utilities

A collection of scripts developed to interact with fasta, fastq and sam/bam files.

oneliners

Useful bash one-liners for bioinformatics.

Phinch

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.

sickle

Windowed Adaptive Trimming for fastq files using quality

biopython

Official git repository for Biopython (originally converted from CVS)

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

RAPSearch2

Reduced Alphabet based Protein similarity Search

pullseq

Utility program for extracting sequences from a fasta/fastq file

CONCOCT

Clustering cONtigs with COverage and ComposiTion

khmer-protocols

literate-resting

Scripts and code for development of literate testing with reST-based shell tutorials.

2013-intro-computational-science

PhyloSift

Phylogenetic and taxonomic analysis for genomes and metagenomes

ray

Ray -- Parallel genome assemblies for parallel DNA sequencing

picante

R tools for integrating phylogenies and ecology