Keywords
bioinformatics, toolkit, command-line
This article is included in the Bioinformatics gateway.
This article is included in the Python collection.
bioinformatics, toolkit, command-line
There are of course 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. But 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. Rather it is a collection that has been built (and is still being built) over several years. Anytime I need to write something to perform a task that has more than a one-off ad hoc use, something I end up using frequently, I consider adding it to the bit package. Some programs are light wrappers that extend and/or simplify the utility of existing software (like taxonkit4 and goatools5); many are written in Python leveraging the Biopython6 module (e.g. programs to summarize assemblies, calculate gc content, calculate Shannon uncertainty per column in multiple sequence alignments, pulling amino-acid sequences from GenBank files); and many are bash scripts to do things like download any assembly in 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.
The package is written in Bash and Python (3+), and is built to run in a Unix-like environment.
bit is packaged in conda,8 which serves as its primary means of installation. All dependencies are handled by the conda installation, but they include: python v3+; biopython6 v1.7.9+; pybedtools9 v0.8.2+; GNU parallel10 v20211022+; pandas11 v1.3.4+; entrez direct12 v16.2+; taxonkit4 v0.9.0+; goatools5 v0.8.12.
All commands are prefixed with ‘bit-’ and so can be seen by typing that and hitting tab twice. Each comes with a help menu by running the command with no arguments or with ‘-h’. In Figure 1 is an example with the program for downloading genome assemblies from NCBI by providing accessions.
Source code available from: https://www.github.com/AstrobioMike/bit.
Archived analysis code as at time of publication: https://doi.org/10.5281/zenodo.3383647.
License: GNU GPL v3.0.
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Is the rationale for developing the new software tool clearly explained?
No
Is the description of the software tool technically sound?
No
Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others?
No
Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool?
No
Are the conclusions about the tool and its performance adequately supported by the findings presented in the article?
No
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Bioinformatics, Artificial Intelligence, Machine Learning, Data Mining, Data Visualization
Is the rationale for developing the new software tool clearly explained?
No
Is the description of the software tool technically sound?
No
Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others?
Partly
Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool?
No
Are the conclusions about the tool and its performance adequately supported by the findings presented in the article?
No
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Bioinformatics, single-cell genomics
Alongside their report, reviewers assign a status to the article:
Invited Reviewers | ||
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Version 1 31 Jan 22 |
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Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list:
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