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sanger-tol/genomeassembly: 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: https://doi.org/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: https://doi.org/10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

  • Hifiasm

    Cheng, H., Concepcion, G.T., Feng, X. et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). doi: https://doi.org/10.1038/s41592-020-01056-5

  • purge_dups

    Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020 May 1;36(9):2896-2898. doi: https://doi.org/10.1093/bioinformatics/btaa025. PMID: 31971576; PMCID: PMC7203741.

  • Longranger

  • Freebayes

    Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012

  • bwa-mem2

    Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. doi: https://doi.org/10.1109/IPDPS.2019.00041

  • YaHS

    Chenxi Zhou and others, YaHS: yet another Hi-C scaffolding tool, Bioinformatics, Volume 39, Issue 1, January 2023, btac808, doi: https://doi.org/10.1093/bioinformatics/btac808

  • Minimap2

    Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics. 2021 Oct 8;37(23):4572–4. doi: https://doi.org/10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391; PMCID: PMC8652018.

  • Samtools

    Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: https://doi.org/10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819.

  • Bcftools

    Danecek P, Bonfield JK, et al. Twelve years of SAMtools and BCFtools. Gigascience (2021) 10(2):giab008 link

  • GATK4

    Van der Auwera GA & O'Connor BD. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (1st Edition). O'Reilly Media.

  • Bedtools

    Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: https://doi.org/10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PMID: 20110278; PMCID: PMC2832824.

  • Juicer

    Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016 Jul;3(1):95-8. doi: https://doi.org/10.1016/j.cels.2016.07.002. PMID: 27467249; PMCID: PMC5846465.

  • PretextMap

  • Cooler

    Abdennur N, Mirny LA. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020 Jan 1;36(1):311-316. doi: https://doi.org/10.1093/bioinformatics/btz540. PMID: 31290943; PMCID: PMC8205516.

  • MitoHiFi

    MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads Marcela Uliano-Silva, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Darwin Tree of Life Consortium, Giulio Formenti, Linelle Abueg, James Torrance, Eugene W. Myers, Richard Durbin, Mark Blaxter, Shane A. McCarthy bioRxiv 2022.12.23.521667; doi: https://doi.org/10.1101/2022.12.23.521667

  • MitoFinder

    Allio, R, Schomaker‐Bastos, A, Romiguier, J, Prosdocimi, F, Nabholz, B, Delsuc, F. MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020; 00: 1– 14. doi: https://doi.org/10.1111/1755-0998.13160

  • MITOS

    M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, P. F. Stadler MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation Molecular Phylogenetics and Evolution 2013, 69(2):313-319.

  • MerquryFK

  • BUSCO

    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

  • GFASTATS

    Giulio Formenti and others, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, doi: https://doi.org/10.1093/bioinformatics/btac460

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: https://doi.org/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: https://doi.org/10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

  • Singularity

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