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psmc

punchcard

Generate GitHub-style punchcard charts with ease.

pybwa

Python libraries to interact with BWA mapper

pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

python_for_data_science

A rapid on-ramp primer for programmers who want to learn Python for doing data science research and development.

pythontidy

Fork of Chuck Rhode's PythonTidy script.

q2oligo

Convert QIIME files into Oligotyping subsets.

qiime

Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests

quick_basic_r_tutorial

This is a quick and basic tutorial for R

r-gis-tutorial

Spatial data in R: using R as a GIS

readuntangler

refweak

A list of weak Bacterial assemblies in GenBank

reimagined_chowder

Robot's reimagining of soups and stews

reviews

Writing reviews of academic papers

rforecastio

Simple R interface to forecast.io weather data

rna-deseq2

Template for DESeq2 Analysis of RNA-seq data

rphylip

An R interface for PHYLIP.

rst2html5

transform restructuredtext documents to html5 + twitter's bootstrap css, deck.js or reveal.js

rusda

Interface to USDA Databases

sabre

samtools

This is the official development repository for samtools.

seqprep

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

seqtk

Toolkit for processing sequences in FASTA/Q formats

sff2fastq

extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

shmlast

blast, shmlast

sibelia

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.

simseq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

site

Software Carpentry web site.

solarplot

Mitochondrial Solar Plot

sql-ecology

Lesson on using the SQL for ecology