SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

TileQC: A system for tile-based quality control of Solexa data

(2008) Peter C Dolan et al.   BMC BIOINFORMATICS