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This module is designed to remove regions of poor quality in 454 sequence data. Drops in quality can be visualized with the quality_scores_plot.py module. The base position specified will be used as an index to truncate the sequence and quality scores, and all data at that base position and to the end of the sequence will be removed in the output filtered files.
Usage: truncate_fasta_qual_files.py [options]
Filtered versions of the input fasta and qual file (based on input name with ‘_filtered’ appended) will be generated in the output directory
Truncate the input fasta and quality files at base position 100, output to the filtered_seqs directory:
truncate_fasta_qual_files.py -f seqs.fna -q seqs.qual -b 100 -o filtered_seqs/