BlastTab.seqdepth.pl
Estimates the sequencing depth of subject sequences.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
- Perl.
§ Usage
BlastTab.seqdepth.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) Median sequencing depth. (4) Number of mapped reads. (5) Length of the subject sequence.