Number of reads mapped to a contig

[JLammons14]

Hello Silas,

I had a quick question for you, sorry if there is already an answer here, but I having been using the contigs generated from ATLAS to identify bacteriophage in my samples. I wanted to know if there is an output in atlas that would tell me how many reads mapped to the bacteriophage contig or some similar metric of abundance.

I saw this post: #186 , regarding a somewhat similar problem but I dont think it quite addresses what I was looking for, so thought I would ask this here.

Thanks for your time, sorry if this info was provided somewhere else.

[SilasK]

I think you need to look at the coverage statistics for each file "{sample}/assembly/contig_stats/postfilter_coverage_stats.txt"`

there is also a binned version of this file. e.g. coverage information for each 1kb window.

I agree this could be better described.