CITATIONS.md

plant-food-research-open/assemblyqc: Citations

nf-core

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

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

• fa-lint, MIT

  https://github.com/GallVp/fa-lint

• GenomeTools, ISC

  Gremme G, Steinbiss S, Kurtz S. 2013. "GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 3, pp. 645-656, May 2013, doi: https://doi.org/10.1109/TCBB.2013.68

• samtools, MIT/Expat

  Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

• NCBI FCS, License

  Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD. 2023. Rapid and sensitive detection of genome contamination at scale with FCS-GX. bioRxiv 2023.06.02.543519; doi: https://doi.org/10.1101/2023.06.02.543519

• Krona, License

  Ondov BD, Bergman NH, Phillippy AM. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385. doi: https://doi.org/10.1186/1471-2105-12-385

• assemblathon_stats, CC BY-NC-SA 3.0

  github/PlantandFoodResearch/assemblathon2-analysis/a93cba2

  Forked from: https://github.com/ucdavis-bioinformatics/assemblathon2-analysis

• gfastats, MIT

  Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D Jarvis, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, https://doi.org/10.1093/bioinformatics/btac460

• BUSCO, MIT

  Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. 2021. 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, https://doi.org/10.1093/molbev/msab199

• GffRead, MIT

  Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: http://doi.org/10.12688/f1000research.23297.2. PMID: 32489650; PMCID: PMC7222033.

• tidk, MIT

  https://github.com/tolkit/telomeric-identifier

• SeqKit, MIT

  Shen W, Le S, Li Y, Hu F. 2016. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE 11(10): e0163962. https://doi.org/10.1371/journal.pone.0163962

• LAI, GPL v3

  Ou S, Chen J, Jiang N. 2018. Assessing genome assembly quality using the LTR Assembly Index (LAI), Nucleic Acids Research, Volume 46, Issue 21, 30 November 2018, Page e126, https://doi.org/10.1093/nar/gky730

• LTR_FINDER_parallel, MIT

  Ou S, Jiang N 2019. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mobile DNA 10, 48 (2019). https://doi.org/10.1186/s13100-019-0193-0

• LTRharvest, ISC

  Ellinghaus, D, Kurtz, S & Willhoeft, U 2008. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9, 18 (2008). https://doi.org/10.1186/1471-2105-9-18

• LTR_retriever, GPL v3

  Shujun O, Ning J 2018. LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons, Plant Physiology, 176, 2 (2018). https://doi.org/10.1104/pp.17.01310

• Kraken 2, MIT

  Wood DE, Salzberg SL, Wood DE, Lu J, Langmead B. 2019. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0

• juicebox.js, MIT

  Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. 2018. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst. 2018 Feb 28;6(2):256-258.e1. doi: https://doi.org/10.1016/j.cels.2018.01.001. Epub 2018 Feb 7. PMID: 29428417; PMCID: PMC6047755.

• fastp, MIT

  Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560

• FastQC, GPL v3

  https://github.com/s-andrews/FastQC

• HapHiC, BSD-3-Clause

  Xingtan Zhang, Shengcheng Zhang, Qian Zhao, Ray Ming, Haibao Tang. (2019) Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nature Plants, 5:833-845. doi: https://doi.org/10.1038/s41477-019-0487-8

• hic_qc, AGPL v3

  https://github.com/phasegenomics/hic_qc/commit/6881c3390fd4afb85009a52918b4d068100c58b4

• JUICEBOX_SCRIPTS, AGPL v3

  https://github.com/phasegenomics/juicebox_scripts/commit/a7ae9915401eb677b8058b0118011ce440999bc0

• bwa-mem, GPL v3

  Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. https://doi.org/10.48550/arXiv.1303.3997

• YaHS, MIT

  Chenxi Zhou, Shane A McCarthy, Richard Durbin, YaHS: yet another Hi-C scaffolding tool, Bioinformatics, Volume 39, Issue 1, January 2023, btac808, https://doi.org/10.1093/bioinformatics/btac808

• hictk, MIT

  Roberto Rossini, Jonas Paulsen, hictk: blazing fast toolkit to work with .hic and .cool files Bioinformatics, Volume 40, Issue 7, July 2024, btae408, https://doi.org/10.1093/bioinformatics/btae408

• samblaster, MIT

  Faust GG, Hall IM. 2014. SAMBLASTER: fast duplicate marking and structural variant read extraction, Bioinformatics, Volume 30, Issue 17, September 2014, Pages 2503–2505, https://doi.org/10.1093/bioinformatics/btu314

• Circos, GPL v3

  Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R. Horsman D, ... Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645. https://doi.org/10.1101/gr.092759.109

• MUMmer, Artistic 2.0

  Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. 2018. MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol. 2018 Jan 26;14(1):e1005944. doi: https://doi.org/10.1371/journal.pcbi.1005944. PMID: 29373581; PMCID: PMC5802927.

• Plotsr, MIT

  Goel M, Schneeberger K. 2022. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics. 2022 May 13;38(10):2922-2926. doi: https://doi.org/10.1093/bioinformatics/btac196. PMID: 35561173; PMCID: PMC9113368.

• Syri, MIT

  Goel M, Sun H, Jiao WB, Schneeberger K. 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019 Dec 16;20(1):277. doi: https://doi.org/10.1186/s13059-019-1911-0. PMID: 31842948; PMCID: PMC6913012.

• Minimap2, MIT

  Li H. 2021. New strategies to improve minimap2 alignment accuracy, Bioinformatics, Volume 37, Issue 23, December 2021, Pages 4572–4574, doi: https://doi.org/10.1093/bioinformatics/btab705

• Merqury, United States Government Work

  Rhie, A., Walenz, B.P., Koren, S. et al. 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245. doi: https://doi.org/10.1186/s13059-020-02134-9

• OrthoFinder, GPL v3

  Emms, D.M., Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20, 238 (2019). doi: 10.1186/s13059-019-1832-y

• Winnowmap, LicenseRef-Public-Domain

  Chirag Jain, Arang Rhie, Nancy Hansen, Sergey Koren and Adam Phillippy. "Long-read mapping to repetitive reference sequences using Winnowmap2". Nature Methods, 2022. doi: 10.1038/s41592-022-01457-8

• T2T-Polish, LicenseRef-Public-Domain

  Mc Cartney AM, Shafin K, Alonge M et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods (2022) doi: 10.1038/s41592-022-01440-3

• bedtools, MIT

  Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, doi: 10.1093/bioinformatics/btq033

• Clair3, Custom Permissive

  Zheng, Z., Li, S., Su, J., Leung, A. W. S., Lam, T. W., & Luo, R. (2022). Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nature Computational Science, 2(12), 797-803. doi: 10.1101/2021.12.29.474431

Software packaging/containerisation tools

• Anaconda

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

• Bioconda

  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

  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

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

• Singularity

  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.