Assembling reads with velvet

Velvet is a hash-based deBrujin assembler. I occasionally use it to build contigs from short read RNAseq data, although it can be used for long reads, metagenomics, etc.

To install, just download, extract and make.

There are two parts to the program:
1. velveth – prepare the sequences
2. velvetg – build the graph and output the contig.fa and some summary statistics

# prepare sequences
velveth contig/ 21 -raw dmd_kmer_matches.txt
# build the graph
velvetg contig/ -min_contig_lgth 100

There are several parameters you can tune.
– kmer length
– coverage cutoff (cov_cutoff)
– minimum contig length (min_contig_lgth)

It can take as input paired end or single end, FASTQ, FASTA and other formats. It is not restricted to illumina output.

velvetg will produce a fasta file of contigs and summary stats.