kmermaid

k-mer similarity analysis pipeline

Science Score: 57.0%

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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DOI references
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Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary

Keywords

k-mer kmer kmer-counting kmer-frequency-count nextflow nf-core pipeline workflow

Keywords from Contributors

metagenomics taxonomic-classification taxonomic-profiling bioinformatics rna-seq 10x-genomics 10xgenomics single-cell pipelines workflows

Last synced: 6 months ago · JSON representation ·

Repository

k-mer similarity analysis pipeline

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: dev
Homepage: https://nf-co.re/kmermaid
Size: 12.8 MB

Statistics

Stars: 21
Watchers: 154
Forks: 13
Open Issues: 21
Releases: 1

Topics

k-mer kmer kmer-counting kmer-frequency-count nextflow nf-core pipeline workflow

Created over 6 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Introduction

nf-core/kmermaid is a bioinformatics pipeline that performs comparative analysis of *omes using k-mer based methods. It supports various reference and sequencing input formats, and provides statistics files along with a MultiQC report as output. It provides pre-processing methods for reads and alignments.

In the outline below, every step except for the main analysis is optional and might be input-dependent.

Optional – BAM preprocessing

Extract BAM from 10X archive (tar)
Extract FASTQ reads (samtools)
Split reads per cell (grep)
Count UMIs per cell (pbtk)
Download SRA experiment () [optional]

Optional – read preprocessing

Trim reads (fastp)
Read QC (FastQC)
Remove rRNA (sortmerna)
Translate to protein (orpheum)

k-mer analysis per method

Create sketch
Calculate distances
Present the results (MultiQC)

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.

Usage

With a samples.csv file

bash nextflow run nf-core/kmermaid --outdir s3://bucket/sub-bucket --samples samples.csv

With R1, R2 read pairs

bash nextflow run nf-core/kmermaid --outdir s3://olgabot-maca/nf-kmer-similarity/ \ --read_pairs 's3://bucket/sub-bucket/*{R1,R2}*.fastq.gz,s3://bucket/sub-bucket2/*{1,2}.fastq.gz'

With SRA ids

bash nextflow run nf-core/kmermaid --outdir s3://bucket/sub-bucket --sra SRP016501

With fasta files

bash nextflow run nf-core/kmermaid --outdir s3://bucket/sub-bucket \ --fastas '*.fasta'

With bam file

bash nextflow run nf-core/kmermaid --outdir s3://bucket/sub-bucket \ --bam 'possorted_genome_bam.bam'

With split kmer

bash nextflow run nf-core/kmermaid --outdir s3://bucket/sub-bucket --samples samples.csv --split_kmer --subsample 1000

Credits

nf-core/kmermaid was originally written by Olga Botvinnik. The DSL2 port is done by Igor Trujnara.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #kmermaid channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

Name: nf-core
Login: nf-core
Kind: organization
Email: core@nf-co.re

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md)

# nf-core/kmermaid: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total

Watch event: 1
Member event: 1
Issue comment event: 7
Push event: 13
Pull request review comment event: 2
Pull request review event: 6
Pull request event: 17
Fork event: 1
Create event: 5

Last Year

Watch event: 1
Member event: 1
Issue comment event: 7
Push event: 13
Pull request review comment event: 2
Pull request review event: 6
Pull request event: 17
Fork event: 1
Create event: 5

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,260
Total Committers: 7
Avg Commits per committer: 180.0
Development Distribution Score (DDS): 0.378

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Olga Botvinnik	o**k@g**m	784
pranathivemuri	p**i@g**m	406
phoenixAja	p**x@p**t	36
lekhakaranam	l**m@M**l	19
Saba Nafees	s**4@g**m	10
MaxUlysse	m**a@g**m	3
nf-core-bot	c**e@n**e	2

Committer Domains (Top 20 + Academic)

nf-co.re: 1 phoenixlogan.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 20
Total pull requests: 85
Average time to close issues: 8 months
Average time to close pull requests: about 1 month
Total issue authors: 6
Total pull request authors: 9
Average comments per issue: 1.75
Average comments per pull request: 1.46
Merged pull requests: 46
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 5
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Issue authors: 0
Pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 0.6
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

olgabot (14)
ewels (2)
pranathivemuri (1)
maxulysse (1)
phoenixAja (1)
apeltzer (1)

Pull Request Authors

olgabot (38)
nf-core-bot (24)
pranathivemuri (15)
lekhakaranam (4)
itrujnara (3)
KevinMenden (2)
maxibor (1)
ewels (1)
phoenixAja (1)

Top Labels

Issue Labels

enhancement (5) bug (2) help wanted (1) good first issue (1)

Pull Request Labels

reviewer can merge (6) Needs review (3)

Dependencies

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modules/nf-core/fastqc/environment.yml pypi

modules/nf-core/multiqc/environment.yml pypi

kmermaid

Science Score: 57.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Introduction

Usage

With a samples.csv file

With R1, R2 read pairs

With SRA ids

With fasta files

With bam file

With split kmer

Credits

Contributions and Support

Citations

Owner

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies