FastA.filterN.pl
Filter sequences by N-content and presence of long homopolymers.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
- Perl.
§ Usage
FastA.filterN.pl in_file float [opts] > out_file
§ Arguments
- Sequences*
in_file
Input file in FastA format.- Content*
float
A number between 0 and 1 indicating the maximum proportion of Ns (1 to turn off, 0.5 by default).- Stretch
integer
A number indicating the maximum number of consecutive identical nucleotides allowed (0 to turn off, 100 by default).- Filtered*
out_file
Filtered set of sequences.