interpretation Abyss stats

Question

[milanlove]

i used Abyss to assemble some reads and after assembly, it give me stats like this:

n:114915

min:500

n50:739

sum:2471869

it say me that minimum contig size is 500 while in output fasta file i see contigs less than 500. it confused me. also when i use grep command (grep -v ">" input.fasta | wc | awk '{print $3-$1}') to get nucleotide count it give me 17458192 that is so bigger than 2471869. what is problem?

[macmath]

Could you provide more details of the parameters used or any log information

Answer 1

[benv]

Hi Sej,

Sorry for the late reply.

When calculating stats such as N50 and sum (a.k.a. reconstruction), ABySS discards all sequences below a minimum length threshold (default value: 500 bp). This is usual practice in the assembly domain because de novo assemblies typically contain a subset of "junk" sequences that are very short (e.g. k bp), and are caused by a mixture of: sequencing errors, uncollapsed heterozygosity, and unresolved repeat sequences.

The min field reported by ABySS is the length of the shortest sequence that is above or equal to the length cutoff (default value: 500 bp).

Stats in ABySS are calculated by the abyss-fac program. If you want to calculate stats with a different minimum length cutoff, you can run abyss-fac on your FASTA file and specify a different cutoff with the -t option.

For a more detailed description of the stats reported by ABySS, please see: https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#stats

[milanlove]

your answer is complete, thanks a lot

Answer 2

[Sej Modha]

Maybe this would help? https://groups.google.com/forum/#!topic/abyss-users/OzyeFhfxuFU