Abstract
bit is a collection of small scripts and programs that facilitate many common tasks in bioinformatics. It operates in a Unix-like command-line environment and is comprised of bash and python code. bit is openly available on GitHub, archived with Zenodo, and is conda installable. The package is useful for users who want to do things such as manipulate fasta files, calculate GC content, quickly summarize nucleotide assemblies, easily download assemblies from NCBI just based on accessions, pull amino-acid sequences from GenBank files, calculate Shannon uncertainty for columns in multiple sequence alignments, and more. The source code is hosted on GitHub: github.com/AstrobioMike/bit
Highlights
There are several great and widely used packages of bioinformatics helper programs already available
Some of these include the likes of seqtk,[1] fastX-toolkit,[2] and bbtools3 – all of which I use regularly and have facilitated goals I was trying to accomplish
There are always more tasks that crop up that may not yet have a helper program or script already written to accomplish them. bit is a collection of small scripts and programs that were not written for any single piece of research work
Summary
There are several great and widely used packages of bioinformatics helper programs already available. Some of these include the likes of seqtk,[1] fastX-toolkit,[2] and bbtools3 – all of which I use regularly and have facilitated goals I was trying to accomplish. There are always more tasks that crop up that may not yet have a helper program or script already written to accomplish them. Different file formats from NCBI7 just by providing a list of wanted accessions. It is a rather random collection, but it is of convenience to many users
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