GATB: Genome Assembly & Analysis Tool Box

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

(2014) Kamil Salikhov et al.   Algorithms for Molecular Biology

NGS++: a library for rapid prototyping of epigenomics software tools

(2013) A. Nordell Markovits et al.   BIOINFORMATICS

DSK: k-mer counting with very low memory usage

(2013) G. Rizk et al.   BIOINFORMATICS

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing

(2013) Shanrong Zhao et al.   BMC GENOMICS

CRAC: an integrated approach to the analysis of RNA-seq reads

(2013) Nicolas Philippe et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform

(2012) Yongchao Liu et al.   BIOINFORMATICS

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

GASSST: global alignment short sequence search tool

(2010) Guillaume Rizk et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH