FastqUpdate.py:
Updates old Illumina FASTQ files to the new Illumina/Sanger 1.9 FASTQ encoding format. Requires biopython.
gc_parser.pl:
Parses multifasta files by their GC content. Useful to parse out contaminants from genome assemblies.
keep_longest_reads.pl: Calculates metrics for FASTQ file(s) and/or parses them to keep the longest reads either by minimum size or by desired sequencing depth (useful for large Nanopore or PacBio datasets).
read_len_plot.py: Plots the read length distribution for a given FASTQ dataset with matplotlib.
run_pilon.pl: Runs Pilon read correction in paired-end mode for X iterations (stops automatically if Pilon no longer makes changes to the consensus)
runTaxonomizedBLAST.pl: Runs taxonomized BLAST searches, and returns the outfmt 6 format with columns staxids, sscinames, sskingdoms, and sblastnames.
parseTaxonomizedBLAST.pl: Parses the content of BLAST searches performed with runTaxonomizedBLAST.pl.