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Literature DB >> 20836074

Using the Velvet de novo assembler for short-read sequencing technologies.

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.

Entities: Disease Species

Mesh：

Year: 2010 PMID： 20836074 PMCID： PMC2952100 DOI： 10.1002/0471250953.bi1105s31

Source DB: PubMed Journal: Curr Protoc Bioinformatics ISSN： 1934-3396

10 in total

1. An Eulerian path approach to DNA fragment assembly.

Authors: P A Pevzner; H Tang; M S Waterman
Journal: Proc Natl Acad Sci U S A Date: 2001-08-14 Impact factor: 11.205

2. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors: Daniel R Zerbino; Ewan Birney
Journal: Genome Res Date: 2008-03-18 Impact factor: 9.043

3. De novo fragment assembly with short mate-paired reads: Does the read length matter?

Authors: Mark J Chaisson; Dumitru Brinza; Pavel A Pevzner
Journal: Genome Res Date: 2008-12-03 Impact factor: 9.043

4. ABySS: a parallel assembler for short read sequence data.

Authors: Jared T Simpson; Kim Wong; Shaun D Jackman; Jacqueline E Schein; Steven J M Jones; Inanç Birol
Journal: Genome Res Date: 2009-02-27 Impact factor: 9.043

5. De novo assembly of human genomes with massively parallel short read sequencing.

Authors: Ruiqiang Li; Hongmei Zhu; Jue Ruan; Wubin Qian; Xiaodong Fang; Zhongbin Shi; Yingrui Li; Shengting Li; Gao Shan; Karsten Kristiansen; Songgang Li; Huanming Yang; Jian Wang; Jun Wang
Journal: Genome Res Date: 2009-12-17 Impact factor: 9.043

6. ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Authors: Jonathan Butler; Iain MacCallum; Michael Kleber; Ilya A Shlyakhter; Matthew K Belmonte; Eric S Lander; Chad Nusbaum; David B Jaffe
Journal: Genome Res Date: 2008-03-13 Impact factor: 9.043

7. The Sequence Alignment/Map format and SAMtools.

Authors: Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal: Bioinformatics Date: 2009-06-08 Impact factor: 6.937

Review 8. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Authors: Peter J A Cock; Christopher J Fields; Naohisa Goto; Michael L Heuer; Peter M Rice
Journal: Nucleic Acids Res Date: 2009-12-16 Impact factor: 16.971

9. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.

Authors: Daniel R Zerbino; Gayle K McEwen; Elliott H Margulies; Ewan Birney
Journal: PLoS One Date: 2009-12-22 Impact factor: 3.240

10. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

Authors: Stefan Kurtz; Apurva Narechania; Joshua C Stein; Doreen Ware
Journal: BMC Genomics Date: 2008-10-31 Impact factor: 3.969

10 in total

270 in total

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Authors: Keith A Jolley; Dorothea M C Hill; Holly B Bratcher; Odile B Harrison; Ian M Feavers; Julian Parkhill; Martin C J Maiden
Journal: J Clin Microbiol Date: 2012-07-11 Impact factor: 5.948

2. On genome annotation of Brucellaphage Gadvasu (BpG): discovery of ORFans for integrated systems biology approaches.

Authors: Deepti Chachra; Pushpinder Kaur; Prasad Siddavatam; Prashanth Suravajhala; Hari Mohan Saxena
Journal: Syst Synth Biol Date: 2015-11-21

3. Foxtail mosaic virus: A Viral Vector for Protein Expression in Cereals.

Authors: Clément Bouton; Robert C King; Hongxin Chen; Kasi Azhakanandam; Stéphane Bieri; Kim E Hammond-Kosack; Kostya Kanyuka
Journal: Plant Physiol Date: 2018-06-07 Impact factor: 8.340

Review 4. Computational methods for transcriptome annotation and quantification using RNA-seq.

Authors: Manuel Garber; Manfred G Grabherr; Mitchell Guttman; Cole Trapnell
Journal: Nat Methods Date: 2011-05-27 Impact factor: 28.547

5. The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations.

Authors: Ramesh Arunkumar; Rob W Ness; Stephen I Wright; Spencer C H Barrett
Journal: Genetics Date: 2014-12-30 Impact factor: 4.562

6. Whole-genome sequencing of Klebsiella pneumoniae MDR strain isolated in a Syrian refugee.

Authors: Silvia Angeletti; Eleonora Cella; Alessia Lai; Alessandra Lo Presti; Francesca Antonelli; Alessia Conti; Maurizio Lopalco; Silvia Spoto; Gianguglielmo Zehender; Massimo Ciccozzi
Journal: Pathog Glob Health Date: 2017-04-12 Impact factor: 2.894

7. Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette.

Authors: Nathan J Kenny; Sebastian M Shimeld
Journal: Dev Genes Evol Date: 2012-10-09 Impact factor: 0.900