ABySS and Velvet "number of contigs and contig length in pair-end and single-end datasets"
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.
Why Velvet has excess number of contigs in pair-end case compared to single-end?
Why the N50 contig length of single-end reads using ABySS is so short?
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Abdul Rafay Khan
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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.
I am not familiar with Velvet usage, but if you provide the
abyss-pecommand and verbose log output (add "v=-v" toabyss-pecommand), I could have a look. Output ofabyss-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.