Updating and supplementary materials for this paper

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

Wenyu Zhang, Jiajia Chen, Yang Yang, Yifei Tang, Jing Shang, and Bairong Shen *
Center for Systems Biology, Postbox 206, Soochow University, Suzhou 215006, Jiangsu, China
*corresponding author

The updating of paper can be downloaded here.
(Updating)Figure 1: Overview of de novo short reads assemblers.
Supporting materials: Table S1.doc, Table S2.doc, Package S1

Related information for current NGS genome assemblers
Program Reference
SSAKE Assembling millions of short DNA sequences using SSAKE. PMID: 17158514.
VCAKE Extending assembly of short DNA sequences to handle error. PMID: 17893086.
QSRA QSRA: a quality-value guided de novo short read assembler. PMID: 19239711.
SHARCGS SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. PMID: 17908823.
Newbler Genome sequencing in microfabricated high-density picolitre reactors. PMID: 16056220.
Edena De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. PMID: 18332092.
CABOG Aggressive assembly of pyrosequencing reads with mates. PMID: 18952627.
Shorty Crystallizing short-read assemblies around seeds. PMID: 19208115.
Euler-SR Short read fragment assembly of bacterial genomes. PMID: 18083777.
ALLPATHS ALLPATHS: de novo assembly of whole-genome shotgun microreads. PMID: 18340039.
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. PMID: 19796385.
ALLPATHS-LG High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PMID: 21187386.
Velvet Velvet: algorithms for de novo short read assembly using de Bruijn graphs. PMID: 18349386.
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PMID: 20027311.
Euler-USR De novo fragment assembly with short mate-paired reads: Does the read length matter? PMID: 19056694.
ABySS ABySS: a parallel assembler for short read sequence data. PMID: 19251739. De novo transcriptome assembly with ABySS. PMID: 19528083.
SOAPdenovo De novo assembly of human genomes with massively parallel short read sequencing. PMID: 20019144.
Taipan A fast hybrid short read fragment assembly algorithm. PMID: 19535537.
PCAP long-read assembler Generating a genome assembly with PCAP. PMID: 18428744.
MIRA3 http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page
Seqcons A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. PMID: 19269990.
Forge De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. PMID: 19747388.
SR-ASM http://bioserver.cs.put.poznan.pl/sr-asm-short-reads-assembly-algorithm
LOCAS http://ab.inf.uni-tuebingen.de/software/locas/
Contrail http://sourceforge.net/apps/mediawiki/contrail-bio/index.php?title=Contrail
Ray Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. PMID: 20958248.

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