Enveomics collection

A toolbox for microbial genomics and metagenomics

BlastTab.seqdepth_nomedian.pl

Estimates the sequencing depth of subject sequences. The values reported by this script may differ from those of BlastTab.seqdepth.pl, because this script uses the aligned length of the read while BlastTab.seqdepth.pl uses the aligned length of the subject sequence.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

BlastTab.seqdepth_nomedian.pl cat in_file | [opts] in_file > out_file

§ Arguments

Input file*
 in_file  One or more Tabular BLAST files of reads vs genes (or contigs).
Script
 task 
genes_or_ctgs.fna*
 in_file  A FastA file containing the genes or the contigs (db).
genes_or_ctgs.cov*
 out_file  A tab-delimited file with the following columns: (1) Subject ID. (2) Average sequencing depth. (3) Number of mapped reads. (4) Length of the subject sequence.
* Mandatory.