Bacterial Genomics

wf-paired-end-illumina-assembly: 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

• SPAdes

  Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. May 2012;19(5):455-77. doi:10.1089/cmb.2012.0021

• Trimmomatic

  Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. Aug 1 2014;30(15):2114-20. doi:10.1093/bioinformatics/btu170

• BLAST+

  Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009/12/15 2009;10(1):421. doi:10.1186/1471-2105-10-421

• GTDB-Tk

  Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics. Nov 30 2022;38(23):5315-5316. doi:10.1093/bioinformatics/btac672

• BioPython

  Cock PJ, Antao T, Chang JT, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. Jun 1 2009;25(11):1422-3. doi:10.1093/bioinformatics/btp163

• QUAST

  Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. Apr 15 2013;29(8):1072-5. doi:10.1093/bioinformatics/btt086

• PubMLST

  Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. doi:10.12688/wellcomeopenres.14826.1

• RNAmmer

  Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100-8. doi:10.1093/nar/gkm160

• SAMtools

  Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. Aug 15 2009;25(16):2078-9. doi:10.1093/bioinformatics/btp352

• BWA-MEM

  Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. May 26 2013; arXiv:1303.3997. doi:10.48550/arXiv.1303.3997

• FLASH

  Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. Nov 1 2011;27(21):2957-63. doi:10.1093/bioinformatics/btr507

• BUSCO

  Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. Sep 27 2021;38(10):4647-4654. doi:10.1093/molbev/msab199

• BEDTools

  Quinlan AR. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr Protoc Bioinformatics. Sep 8 2014;47:11.12.1-34. doi:10.1002/0471250953.bi1112s47

• mlst

  Seeman T. mlst. Github: https://github.com/tseemann/mlst

• Prokka

  Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. Jul 15 2014;30(14):2068-9. doi:10.1093/bioinformatics/btu153

• SKESA

  Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology. 2018/10/04 2018;19(1):153. doi:10.1186/s13059-018-1540-z

• Pilon

  Walker BJ, Abeel T, Shea T, et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLOS ONE. 2014;9(11):e112963. doi:10.1371/journal.pone.0112963

• Kraken 2

  Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biology. 2019/11/28 2019;20(1):257. doi:10.1186/s13059-019-1891-0

• Kraken

  Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology. 2014/03/03 2014;15(3):R46. doi:10.1186/gb-2014-15-3-r46

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

• 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.

Citation Information

Citations were created with the help of EndNote and were exported in AMA format.