bit: a multipurpose collection of bioinformatics tools

Michael Lee

doi:10.12688/f1000research.79530.1

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bit: a multipurpose collection of bioinformatics tools

[version 1; peer review: 2 not approved]

Michael Lee

PUBLISHED 31 Jan 2022

Author details Author details

Blue Marble Space Institute of Science, Seattle, Washington, USA

Michael Lee
Roles: Software, Writing – Original Draft Preparation, Writing – Review & Editing

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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

Keywords

bioinformatics, toolkit, command-line

Corresponding author: Michael Lee

Competing interests: No competing interests were disclosed.

Grant information: The author(s) declared that no grants were involved in supporting this work.

Copyright: © 2022 Lee M. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Lee M. bit: a multipurpose collection of bioinformatics tools [version 1; peer review: 2 not approved]. F1000Research 2022, 11:122 (https://doi.org/10.12688/f1000research.79530.1) First published: 31 Jan 2022, 11:122 (https://doi.org/10.12688/f1000research.79530.1) Latest published: 31 Jan 2022, 11:122 (https://doi.org/10.12688/f1000research.79530.1)

Introduction

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.

Methods

Implementation

The package is written in Bash and Python (3+), and is built to run in a Unix-like environment.

Operation

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.

Use cases

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.

Figure 1. Example accessing the help menu and using the program for downloading genome assemblies from NCBI.

Software availability

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.

References

1. Li H: seqtk.Reference Source
2. Hanon GJ: FastX-Toolkit.Reference Source
3. Bushnell B: BBtools.Reference Source
4. Shen W, Ren H: TaxonKit: a practical and efficient NCBI taxonomy toolkit.J. Genet. Genomics. 2021; 48(9): 844–850.
5. Klopfenstein DV, Zhang L, Pedersen BS, et al.: GOATOOLS: A Python library for Gene Ontology analyses. Sci. Rep. 2018; 8: 1–17.
6. Cock PJA, Antao T, Chang JT, et al.: Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009; 25: 1422–1423. Publisher Full Text
7. Leary NAO, Wright MW, Brister JR, et al.: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.2016; 44: 733–745.
8. Anaconda-Team: Anaconda Software Distribution.2016.
9. Dale RK, Pedersen BS, Quinlan AR: Pybedtools: A flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 2011; 27: 3423–3424. PubMed Abstract | Publisher Full Text
10. Tange O: GNU Parallel.2021.
11. Team T pandas development: pandas. Zenodo 2020.
12. Agarwala R, Barrett T, Beck J, et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018; 46: D8–D13.

Comments on this article Comments (0)

Version 1

VERSION 1 PUBLISHED 31 Jan 2022

Author details Author details

Blue Marble Space Institute of Science, Seattle, Washington, USA

Michael Lee
Roles: Software, Writing – Original Draft Preparation, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

The author(s) declared that no grants were involved in supporting this work.

Article Versions (1)

version 1

Published: 31 Jan 2022, 11:122

https://doi.org/10.12688/f1000research.79530.1

Copyright

© 2022 Lee M. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Lee M. bit: a multipurpose collection of bioinformatics tools [version 1; peer review: 2 not approved] F1000Research 2022, 11:122 (https://doi.org/10.12688/f1000research.79530.1)

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Open Peer Review

Current Reviewer Status: ?

Key to Reviewer Statuses VIEW HIDE

ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested

Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.

Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions

Version 1

VERSION 1

PUBLISHED 31 Jan 2022

Views

21

Reviewer Report 23 Mar 2022

Georges Hattab, Department of Mathematics and Computer Science, University of Marburg, Marburg, Hesse, 35032, Germany

Not Approved

https://doi.org/10.5256/f1000research.83522.r128277

The author has put some effort to compile a set of useful scripts. By looking at the number of references alone, it is clear the author lacks knowledge in the field of bioinformatics as many works are left out or ... Continue reading

The author has put some effort to compile a set of useful scripts. By looking at the number of references alone, it is clear the author lacks knowledge in the field of bioinformatics as many works are left out or not even mentioned. Aside from this fact, there is no description of the methodologies that are made available. I would invite the author to see what a normal methods section looks like. Although a practical set of scripts is provided and for the most part well written, there is a fundamental gap in describing and reproducing this work. Moreover, I would invite the author to look up relevant and openly available data sets where use cases can be presented and the usefulness can be demonstrated. In its current state, there is need for more than considerable work to improve this submission.

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

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

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Views

40

Reviewer Report 22 Feb 2022

Kai Zhang, Ludwig Institute for Cancer Research, La Jolla, CA, USA

Not Approved

https://doi.org/10.5256/f1000research.83522.r122738

The author reports a collection of scripts for various bioinformatics tasks. However, the manuscript is too short and lacks important details for me to assess the significance and novelty of this work. The rationale for this study is unclear. The ... Continue reading

The author reports a collection of scripts for various bioinformatics tasks. However, the manuscript is too short and lacks important details for me to assess the significance and novelty of this work. The rationale for this study is unclear. The description of the tool is not enough. I suggest the author add more details to the Methods section and perform a thorough comparison with related tools/packages.

Specific comments:

Need to be more clear about the problems or tasks that this toolkit tries to address. How efficient are these scripts? What are the expected input sizes for your scripts? Have you done any comparison with other similar packages?

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

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

CITE

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Version 1

VERSION 1 PUBLISHED 31 Jan 2022

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	1	2
Version 1 31 Jan 22	read	read

Kai Zhang, Ludwig Institute for Cancer Research, La Jolla, USA
Georges Hattab, University of Marburg, Marburg, Germany

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Reviewer Report

21 Views

23 Mar 2022 | for Version 1

Georges Hattab, Department of Mathematics and Computer Science, University of Marburg, Marburg, Hesse, 35032, Germany

21 Views Cite this report Responses(0)

Not Approved

The author has put some effort to compile a set of useful scripts. By looking at the number of references alone, it is clear the author lacks knowledge in the field of bioinformatics as many works are left out or not even mentioned. Aside from this fact, there is no description of the methodologies that are made available. I would invite the author to see what a normal methods section looks like. Although a practical set of scripts is provided and for the most part well written, there is a fundamental gap in describing and reproducing this work. Moreover, I would invite the author to look up relevant and openly available data sets where use cases can be presented and the usefulness can be demonstrated. In its current state, there is need for more than considerable work to improve this submission.

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

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

Respond to this report

Responses (0)

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Reviewer Report

40 Views

22 Feb 2022 | for Version 1

Kai Zhang, Ludwig Institute for Cancer Research, La Jolla, CA, USA

40 Views Cite this report Responses(0)

Not Approved

The author reports a collection of scripts for various bioinformatics tasks. However, the manuscript is too short and lacks important details for me to assess the significance and novelty of this work. The rationale for this study is unclear. The description of the tool is not enough. I suggest the author add more details to the Methods section and perform a thorough comparison with related tools/packages.

Specific comments:

Need to be more clear about the problems or tasks that this toolkit tries to address. How efficient are these scripts? What are the expected input sizes for your scripts? Have you done any comparison with other similar packages?

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

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

Respond to this report

Responses (0)

[1] 1. Li H: seqtk.Reference Source

[2] 2. Hanon GJ: FastX-Toolkit.Reference Source

[3] 3. Bushnell B: BBtools.Reference Source

[4] 4. Shen W, Ren H: TaxonKit: a practical and efficient NCBI taxonomy toolkit.J. Genet. Genomics. 2021; 48(9): 844–850.

[5] 5. Klopfenstein DV, Zhang L, Pedersen BS, et al.: GOATOOLS: A Python library for Gene Ontology analyses. Sci. Rep. 2018; 8: 1–17.

[6] 6. Cock PJA, Antao T, Chang JT, et al.: Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009; 25: 1422–1423. Publisher Full Text

[7] 7. Leary NAO, Wright MW, Brister JR, et al.: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.2016; 44: 733–745.

[8] 8. Anaconda-Team: Anaconda Software Distribution.2016.

[9] 9. Dale RK, Pedersen BS, Quinlan AR: Pybedtools: A flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 2011; 27: 3423–3424. PubMed Abstract | Publisher Full Text

[10] 10. Tange O: GNU Parallel.2021.

[11] 11. Team T pandas development: pandas. Zenodo 2020.

[12] 12. Agarwala R, Barrett T, Beck J, et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018; 46: D8–D13.

bit: a multipurpose collection of bioinformatics tools

Abstract

Keywords

Introduction

Methods

Implementation

Operation

Use cases

Figure 1. Example accessing the help menu and using the program for downloading genome assemblies from NCBI.

Software availability

References

Comments on this article Comments (0)

Open Peer Review

Comments on this article Comments (0)

Open Peer Review

Reviewer Status

Reviewer Reports

Comments on this article

Browse by related subjects

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