4.8 Review

Sense from sequence reads: methods for alignment and assembly

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

SOAP2: an improved ultrafast tool for short read alignment

Ruiqiang Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

ABySS: A parallel assembler for short read sequence data

Jared T. Simpson et al.

GENOME RESEARCH (2009)

Article Biochemical Research Methods

SHRiMP: Accurate Mapping of Short Color-space Reads

Stephen M. Rumble et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Review Biotechnology & Applied Microbiology

The need for speed

Paul Flicek

GENOME BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Biochemical Research Methods

ZOOM! Zillions of oligos mapped

Hao Lin et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

SOAP: short oligonucleotide alignment program

Ruiqiang Li et al.

BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

High-resolution mapping and characterization of open chromatin across the genome

Alan P. Boyle et al.

Article Biochemistry & Molecular Biology

Short read fragment assembly of bacterial genomes

Mark J. Chaisson et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

ALLPATHS: De novo assembly of whole-genome shotgun microreads

Jonathan Butler et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

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

Heng Li et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

David Hernandez et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

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

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

Article Multidisciplinary Sciences

Accurate whole human genome sequencing using reversible terminator chemistry

David R. Bentley et al.

NATURE (2008)

Article Computer Science, Theory & Methods

Fast BWT in small space by blockwise suffix sorting

Juha Karkkainen

THEORETICAL COMPUTER SCIENCE (2007)

Article Biochemical Research Methods

Extending assembly of short DNA sequences to handle error

William R. Jeck et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing

Juliane C. Dohm et al.

GENOME RESEARCH (2007)

Article Biochemical Research Methods

Optimized design and assessment of whole genome tiling arrays

Stefan Graef et al.

BIOINFORMATICS (2007)

Article Biochemical Research Methods

Efficient q-gram filters for finding all ε-matches over a given length

KR Rasmussen et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2006)

Article Multidisciplinary Sciences

Genome sequencing in microfabricated high-density picolitre reactors

M Margulies et al.

NATURE (2005)

Article Biochemical Research Methods

The many faces of sequence alignment

S Batzoglou

BRIEFINGS IN BIOINFORMATICS (2005)

Article Biochemical Research Methods

Serial BLAST searching

I Korf

BIOINFORMATICS (2003)

Article Biochemical Research Methods

PatternHunter: faster and more sensitive homology search

B Ma et al.

BIOINFORMATICS (2002)