This script takes an aligned fasta file and returns a fast file with gap only columns removed, and all positions preceding the last start and following the earliest finish removed. If the resulting alignment is below a specified length sequences are removed from the alignment and the filter recalculated until a satisfactory length is reached.
python filter_seqs_7.py [aligned fasta]
This script is a lightweight trimmer. It takes in a forward fastq, reverse fastq, and index fastq from a barcoded Illumina run and trims to a specified mean quality score. Requires biopython.
python trim_fastq_v2.py [forward fastq] [reverse fastq] [index fastq]