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An efficient index for the colored, compacted, de Bruijn graph
semi-reference-based short read compression
Rapid sensitive and accurate read mapping via quasi-mapping
An attempt at rustification of the CQF (https://github.com/splatlab/cqf)
Assortment of random, potentially-useful utility functions and classes.
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
A simple pipeline using CGAT framework for benchmarking and analysis.
Prepare Sailfish and Salmon output for downstream analysis
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
Useful tools for working with Salmon output
GitHub clone of SVN repo svn://svn.code.sf.net/p/staden/code/io_lib (cloned by http://svn2github.com/)
Aggregate results from bioinformatics analyses across many samples into a single report.
Super fast C++ logging library.
Get the "signature" of fasta files
Methods for the automated discovery of hierarchically-structured chromatin domains
Improved multi-sample transcript abundance estimates using adaptive priors
Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
A succinct colored dBG representation
Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.
Implementing Succinct Data Structures from Sebastiano Vigna(http://sux.di.unimi.it)
Example of how continuous analysis can be used for RNA-Seq differential expression.