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.
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
For a more detailed description of the stats reported by ABySS, please see: https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#stats
modified 3.5 years ago
3.5 years ago by
benv • 720