a parent repo for tools written by I.N.Z during their tenure at the Fire Lab
for adding new sequences to Kraken2 databases (see repo)
for merging outputs from Bracken into OTU tables with the option to sum subsets of the outputs (see repo)
for sorting and length-based filtering of FASTA formatted sequences, also produces single-line output of an input FASTA - good for CLI work
a draft script for omitting sequences from MSAs that contribute to weakly supported insertions (given a reference set of sequences)
a simple script that doubles input FASTA formatted sequences (must be single-line)
a simple bash script based on bioawk that checks if two .fastx files have exactly matching sequences in the same positions - used to check if fastp made a duplication error
a simple python script that counts k-mer matches between reference database and query .fasta files, optionally returning all non-matching query sequences. Designed originally for sequencing adapter decontamination by AZF.