VelvetOptimiser 2.2.5 – Automatically Optimise Velvet Assembler Parameters

VelvetOptimiser 2.2.5

:: DESCRIPTION

VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.

::DEVELOPER

Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl
  • Velvet

:: DOWNLOAD

 VelvetOptimiser

:: MORE INFORMATION

VelvetK 20120606 – Find a reasonable K-mer size to Assemble Genome Reads with Velvet

VelvetK 20120606

:: DESCRIPTION

VelvetK can estimate the best k-mer size to use for your Velvet de novo assembly. It needs two inputs: the estimated genome size, and all your sequence read files. The genome size can be supplied as as a number (eg. 3.5M) or as a FASTA file of a closely related genome.

::DEVELOPER

Torsten Seemann <torsten.seemann@monash.edu>,Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 VelvetK

:: MORE INFORMATION

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 at the European Bioinformatics Institute (EMBL-EBI)

:: 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.

Velvet-SC 0.7.62 – Velvet modified for Single Cell reads

Velvet-SC 0.7.62

:: DESCRIPTION

Velvet-SC is a Velvet modified software for Single Cell reads

::DEVELOPER

UCSD Department of Computer Science and Engineering

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  Velvet-SC

:: MORE INFORMATION

Citation

Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L. Dupont, Jonathan H. Badger, Mark Novotny, Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff, Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner, Roger S. Lasken.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
Nature Biotechnology, vol. 29, no. 11, pp. 915-921 (2011), advance online publication, 18 Sep 2011