A naive implementation of a k-mer counter in Python, takes fasta files and k-mer length requests and outputs all k-mers of length k, their reverse complement, and their frequency within their respective sequence for each sequence in the file.
This package enables you to deal with biological sequence files easily.
omicR It creates fasta files, downloads genomes from NCBI using the refseq number, creates databases to run BLAST+, runs BLAST+ and filters these results to obtain the best match per sequence. These scripts can be used to run BLAST alignment of short-read (DArTseq data). It only works with BLAST V 2.7 or under.
Python Scripts for Haim Lab (Microbiology Research) Projects
Removes duplicate sequences in multifasta file
Parse CSV files containing fasta components to a true fasta file.
fdemux is a FASTA/FASTQ demultiplexer with support for (arbitrarily) fuzzy barcode matching, asymmetric barcoding, and parallel processing.
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