ABySS 2.3.2 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.3.2

:: DESCRIPTION

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinformatics. 2015 Jul 25;16(1):230. doi: 10.1186/s12859-015-0663-4. PMID: 26209068; PMCID: PMC4515008.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.
Konnector v2.0: pseudo-long reads from paired-end sequencing data.
BMC Med Genomics. 2015;8 Suppl 3(Suppl 3):S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504; PMCID: PMC4582294.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

Phred/Phrap/Consed 29.0 – DNA Sequence Assembler & Finishing Tools

Phred/Phrap/Consed 29.0

:: DESCRIPTION

Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.

Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.

::DEVELOPER

Laboratory of PHIL GREEN

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Mac OsX

:: DOWNLOAD

Phred/Phrap/Consed

:: MORE INFORMATION

Citation:

Velvet 1.2.10 – Sequence Assembler for Very Short Reads

Velvet 1.2.10

:: DESCRIPTION

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454.Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

::DEVELOPER

Daniel Zerbino and Ewan Birney

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Velvet

:: MORE INFORMATION

Citation

D.R. Zerbino and E. Birney.
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Research 18:821-829.

BioSequenceAssembler 2.0 – Microsoft Research Sequence Assembler

BioSequenceAssembler 2.0

:: DESCRIPTION

BioSequenceAssembler is intended for use by biologist and laboratory technicians who are responsible for managing next-generation genomic sequencing data for alignment, assembly, and/or BLAST identification.

::DEVELOPER

Microsoft Biology Initiative

:: SCREENSHOTS

BioSequenceAssembler

:: REQUIREMENTS

  • Windows
  • .NET

:: DOWNLOAD

   BioSequenceAssembler

:: MORE INFORMATION