Adaptive reference-free compression of sequence quality scores

Compression of FASTQ and SAM Format Sequencing Data

(2013) James K. Bonfield et al.   PLoS One

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

(2012) A. J. Cox et al.   BIOINFORMATICS

SCALCE: boosting sequence compression algorithms using locally consistent encoding

(2012) Faraz Hach et al.   BIOINFORMATICS

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Compression of next-generation sequencing reads aided by highly efficient de novo assembly

(2012) Daniel C. Jones et al.   NUCLEIC ACIDS RESEARCH

Lightweight algorithms for constructing and inverting the BWT of string collections

(2012) Markus J. Bauer et al.   THEORETICAL COMPUTER SCIENCE

Transformations for the compression of FASTQ quality scores of next-generation sequencing data

(2011) Raymond Wan et al.   BIOINFORMATICS

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Balancing and clustering of words in the Burrows–Wheeler transform

(2010) Antonio Restivo et al.   THEORETICAL COMPUTER SCIENCE

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

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH