Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies
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Open Access
- 1 September 2010
- journal article
- unit
- Published by Wiley in Current Protocols in Bioinformatics
- Vol. 31 (1) , 11.5.1-11.5.12
- https://doi.org/10.1002/0471250953.bi1105s31
Abstract
The Velvet de novo assembler was designed to build contigs and eventually scaffolds from short‐read sequencing data. This protocol describes how to use Velvet, interpret its output, and tune its parameters for optimal results. It also covers practical issues such as configuration, using the VelvetOptimiser routine, and processing colorspace data. Curr. Protoc. Bioinform. 31:11.5.1‐11.5.12. © 2010 by John Wiley & Sons, Inc.Keywords
This publication has 10 references indexed in Scilit:
- Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo AssemblerPLOS ONE, 2009
- De novo assembly of human genomes with massively parallel short read sequencingGenome Research, 2009
- The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variantsNucleic Acids Research, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- ABySS: A parallel assembler for short read sequence dataGenome Research, 2009
- De novo fragment assembly with short mate-paired reads: Does the read length matter?Genome Research, 2008
- A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomesBMC Genomics, 2008
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphsGenome Research, 2008
- ALLPATHS: De novo assembly of whole-genome shotgun microreadsGenome Research, 2008
- An Eulerian path approach to DNA fragment assemblyProceedings of the National Academy of Sciences, 2001