genomeassembler
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
Science Score: 67.0%
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Repository
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
Basic Info
- Host: GitHub
- Owner: nf-core
- License: mit
- Language: Nextflow
- Default Branch: master
- Homepage: https://nf-co.re/genomeassembler
- Size: 4.7 MB
Statistics
- Stars: 26
- Watchers: 172
- Forks: 18
- Open Issues: 5
- Releases: 3
Topics
Metadata Files
README.md
Introduction
nf-core/genomeassembler is a bioinformatics pipeline that carries out genome assembly, polishing and scaffolding from long reads (ONT or pacbio). Assembly can be done via flye or hifiasm, polishing can be carried out with medaka (ONT), or pilon (requires short-reads), and scaffolding can be done using LINKS, Longstitch, or RagTag (if a reference is available). Quality control includes BUSCO, QUAST and merqury (requires short-reads).
Currently, this pipeline does not implement phasing of polyploid genomes or HiC scaffolding.
Usage
[!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 testbefore running the workflow on actual data.
First, prepare a samplesheet with your input data that looks as follows:
samplesheet.csv:
csv
sample,ontreads,hifireads,ref_fasta,ref_gff,shortread_F,shortread_R,paired
sampleName,ontreads.fa.gz,hifireads.fa.gz,assembly.fasta.gz,reference.fasta,reference.gff,short_F1.fastq,short_F2.fastq,true
Each row represents one genome to be assembled. sample should contain the name of the sample, ontreads should contain a path to ONT reads (fastq.gz), hifireads a path to HiFi reads (fastq.gz), ref_fasta and ref_gff contain reference genome fasta and annotations. shortread_F and shortread_R contain paths to short-read data, paired indicates if short-reads are paired. Columns can be omitted if they contain no data, with the exception of shortread_R, which needs to be present if shortread_F is there, even if it is empty.
Now, you can run the pipeline using:
bash
nextflow run nf-core/genomeassembler \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>
[!WARNING] Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow option can be used to provide any configuration except for parameters; see docs.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
Pipeline output
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
Credits
nf-core/genomeassembler was originally written by Niklas Schandry, of the Faculty of Biology of the Ludwig-Maximilians University (LMU) in Munich, Germany.
I thank the following people for their extensive assistance and constructive reviews during 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 #genomeassembler channel (you can join with this invite).
Citations
If you use nf-core/genomeassembler for your analysis, please cite it using the following doi: 10.5281/zenodo.14986998
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/genomeassembler: 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 ### Preprocessing - [lima](https://github.com/pacificbiosciences/barcoding/) - [nanoq](https://github.com/esteinig/nanoq) > Steinig and Coin (2022). Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7(69), 2991, https://doi.org/10.21105/joss.02991 - [porechop](https://github.com/rrwick/Porechop) > Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 2017;3(10):e000132. Published 2017 Sep 14. doi:10.1099/mgen.0.000132 - [TrimGalore](https://github.com/FelixKrueger/TrimGalore) > Felix Krueger, Frankie James, Phil Ewels, Ebrahim Afyounian, Michael Weinstein, Benjamin Schuster-Boeckler, Gert Hulselmans, & sclamons. (2023). FelixKrueger/TrimGalore. Zenodo. https://doi.org/10.5281/zenodo.7598955 ### Assembly - [hifiasm](https://github.com/chhylp123/hifiasm) > Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. (2021) Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 18:170-175. https://doi.org/10.1038/s41592-020-01056-5 > Cheng, H., Jarvis, E.D., Fedrigo, O., Koepfli, K.P., Urban, L., Gemmell, N.J., Li, H. (2022) Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology, 40:1332–1335. https://doi.org/10.1038/s41587-022-01261-x > Cheng, H., Asri, M., Lucas, J., Koren, S., Li, H. (2024) Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods, 21:967-970. https://doi.org/10.1038/s41592-024-02269-8 - [flye](https://github.com/mikolmogorov/Flye) > Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner "metaFlye: scalable long-read metagenome assembly using repeat graphs", Nature Methods, 2020 doi:10.1038/s41592-020-00971-x > Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8 > Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W Shen, Mark Chaisson and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using de Bruijn Graphs", PNAS, 2016 doi:10.1073/pnas.1604560113 ### Polishing - [pilon](https://github.com/broadinstitute/pilon) > Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl (2014) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11): e112963. doi:10.1371/journal.pone.0112963 - [medaka](https://github.com/nanoporetech/medaka) ### Scaffolding - [LINKS](https://github.com/bcgsc/LINKS) > Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, Birol I (2015) LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015 - [longstitch](https://github.com/bcgsc/longstitch) > Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL and Birol I. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics 22, 534 (2021). https://doi.org/10.1186/s12859-021-04451-7 - [RagTag](https://github.com/malonge/RagTag) > Alonge, Michael, et al. "Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing." Genome Biology (2022). https://doi.org/10.1186/s13059-022-02823-7 ### Annotation liftover - [liftoff](https://github.com/agshumate/Liftoff) > Shumate, Alaina, and Steven L. Salzberg. 2020. “Liftoff: Accurate Mapping of Gene Annotations.” Bioinformatics , December. https://doi.org/10.1093/bioinformatics/btaa1016 ### Quality control - [BUSCO](https://busco.ezlab.org/) > Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov, BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654 - [genomescope2](https://github.com/tbenavi1/genomescope2.0) > Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11, 1432 (2020). https://doi.org/10.1038/s41467-020-14998-3 > Vurture, GW, Sedlazeck, FJ, Nattestad, M, Underwood, CJ, Fang, H, Gurtowski, J, Schatz, MC (2017) Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btx153 - [jellyfish](https://github.com/gmarcais/Jellyfish) > Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 doi:10.1093/bioinformatics/btr011 - [meryl](https://github.com/marbl/meryl) and [merqury](https://github.com/marbl/merqury) > Rhie, A., Walenz, B.P., Koren, S. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020). https://doi.org/10.1186/s13059-020-02134-9 - [QUAST](https://github.com/ablab/quast) > Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics (2013) 29 (8): 1072-1075. doi: 10.1093/bioinformatics/btt086 ### Mapping - [minimap2](https://github.com/lh3/minimap2) > Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. doi:10.1093/bioinformatics/bty191 > Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. doi:10.1093/bioinformatics/btab705> - [samtools](https://github.com/samtools/samtools) > Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li (2021) Twelve years of SAMtools and BCFtools. GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008 ## 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. - [charliecloud](https://hpc.github.io/charliecloud/) > Reid Priedhorsky and Tim Randles. “Charliecloud: Unprivileged containers for user-defined software stacks in HPC”, 2017. In Proc. Supercomputing. DOI: 10.1145/3126908.3126925.
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- Member event: 1
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Last Year
- Create event: 12
- Release event: 3
- Issues event: 63
- Watch event: 10
- Delete event: 8
- Member event: 1
- Issue comment event: 168
- Push event: 109
- Pull request review comment event: 219
- Pull request review event: 252
- Pull request event: 153
- Fork event: 8
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| Name | Commits | |
|---|---|---|
| Mahesh Binzer-Panchal | m****l@n****e | 113 |
| nf-core-bot | c****e@n****e | 7 |
| daniel | d****b@g****m | 3 |
| Matthieu Muffato | m****9@s****k | 2 |
| d4straub | d****b@u****e | 1 |
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- Average time to close issues: 12 days
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- Average comments per issue: 1.84
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- Merged pull requests: 64
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