Question: ABySS and Velvet "number of contigs and contig length in pair-end and single-end datasets"
gravatar for Abdul Rafay Khan
2.8 years ago by
Karachi, PK
Abdul Rafay Khan1.1k wrote:

I have run Velvet and ABySS using default parameters on my pair-end and single-end datasets, I have two questions related to the generated contigs.

  1. Why Velvet has excess number of contigs in pair-end case compared to single-end?

  2. Why the N50 contig length of single-end reads using ABySS is so short?

velvet abyss ngs illumina • 1.1k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Abdul Rafay Khan1.1k

There could be a number of different things that might have led to this results such as k-mer size for the assembly, quality of the single vs paired-end data and a bunch of other parameters that could have been used to build the assemblies.

ADD REPLYlink written 2.8 years ago by Sej Modha4.7k

I am not familiar with Velvet usage, but if you provide the abyss-pe command and verbose log output (add "v=-v" to abyss-pe command), I could have a look. Output of abyss-fac (N50 etc.) is helpful as well.

It is standard practice to run assemblies for a range of k-mer sizes to achieve the best possible results.

ADD REPLYlink written 2.8 years ago by benv710
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