Results for "Velvet"
Blogs
Protocol for De novo Genome Assembly using Illumina Reads
...ant range of short-read assemblers are available. Everyone with strengths and disadvantages of their own. Some of the assemblers available include:VelvetSOAP-denovoMIRAALLPATHS Next...1201 days ago
Bookmarks
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
...lters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...1215 days ago
VAGUE:Velvet Assembler Graphical Front End
VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginn...2623 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...mes from fastq files in a short time and produces assemblies similar to Velvet or Ray in quality. LACHESIS...e coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreov...2682 days ago
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...-throughput sequencing datasets with non-uniform coverage. Medvedev et al., Bioinformatics 27(13):i137-41, 2011. PubMedCentral De novo assembly Velvet: algorithms for de novo short...3776 days ago
Commercial and public next-gen-seq (NGS) software
...the SOAP suite. See above. VCAKE - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE. Velvet - Velvet is a de novo genomic assemble...3515 days ago
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Comparison of Short Read De Novo Alignment Algorithms
Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil GopalTags: Sequencing, assembly, de novo assembly, velvet
3906 days ago
Standardized velvet assembly report
Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, ad...Tags: Bioinformatics, Analysis, Assembly, Genome, Velvet, standardized-velvet-assembly-report
2701 days ago
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Comments
- Velvet advicer http://dna.med.monash.edu.au/~torsten/velvet_advisor/
2701 days ago
Comment on "Commercial and public next-gen-seq (NGS) software"
There are several other softwares Eland: http://illumina.ucr.edu/illumina_docs/Velvet:http://www.ebi.ac.uk/~zerbino/velvet/Maq (Mapping and Assembly with Quality): http://maq.sourceforge.net/maq-man.s...3618 days ago
