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This is the CURRENT version of the manual (which may not match the version we have installed).Some simple commands to run velvet (
Simple Velvet commands for paired-end illumina data
There are many options for all these commands that can be played around with, but these are the most basic assembly instructions).
For paired-end illumina data:
1. Preprocess the illumina fastq files - Velvet needs the R1 and R2 reads in one single file.
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shuffleSequences_fastq.pl R1.fastq R2.fastq > R1_R2.fastq &
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2. Make hash of the reads using Velveth. Hash length (or kmer length) matters. You might have to run velvet several times to pick the best kmer length. It should be long enough to avoid false positives, but not long that you miss out reads in your assembly. Recommendation: try k-mer lengths between 61-73.
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Contigs.fa will have all the contigs that were assembled. The contig header will have information such as length and coverage for that contig.
Note that the length and coverage information provided in the header of each contig should be understood in k-mers and in k-mer coverage respectively. E.g. for a 500bp contig and a k-mer length of 21, the length in the header will be 480.
To pull out the top 50 largest contig headers:
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