CITATIONS.md

biodiversitycellatlas/bca_preprocessing: Citations

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.

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.

Pipeline tools

• Alevin

  Srivastava, A., Malik, L., Smith, T. et al. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biol 20, 65 (2019).

• Alevin-fry

  He, D., Zakeri, M., Sarkar, H. et al. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022).

• CellBender

  Stephen J Fleming, Mark D Chaffin, Alessandro Arduini et al. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nature Methods, 2023. https://doi.org/10.1038/s41592-023-01943-7

• CellSweep

  Maya Caskey, Joseph Rich, Ryan Weber et al. Single-Cell Genomics Decontamination with CellSweep. bioRxiv 2026.03.04.709349, doi: https://doi.org/10.64898/2026.03.04.709349.

• fastp

  Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.

• FastQC

  Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data.

• featureCounts

  Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.

• Kraken2

  Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0

• matplotlib

  J. D. Hunter. (2007). Matplotlib: A 2D Graphics Environment, Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95. https://ieeexplore.ieee.org/document/4160265

• MultiQC

  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.

• numpy

  Harris, C.R., Millman, K.J., van der Walt, S.J. et al. (2020).Array programming with NumPy. Nature 585, 357–362 (2020). https://doi.org/10.1038/s41586-020-2649-2

• pandas

  pandas development team. (2021). pandas-dev/pandas: Pandas (v2.1.0rc0). Zenodo. https://doi.org/10.5281/zenodo.605272

• pigz

  The pigz developement team. (2023). pigz: A parallel implementation of gzip for modern multi-processor, multi-core machines.

• pysam

  pysam: a Python module for reading and manipulating SAM/BAM files.

• Salmon

  Patro, R., Duggal, G., Love, M. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417–419 (2017).

• SAMtools

  Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

• seqtk

  Li, H. et al. (2023). Seqtk: a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.

• Simpleaf

  He, D., Patro, R. simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry, Bioinformatics 39, 10 (2023).

• STARsolo

  Benjamin Kaminow, Dinar Yunusov, Alexander Dobin. STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. BioRxiv 2021.05.05.442755 (2021).

Git modules

• 10x_saturate

  Zolotarov, G., Elek, A. (2024). 10x_saturate: Compute sample saturation curve by downsampling.

• GeneExt

  Zolotarov, G., Grau-Bové, X., & Sebé-Pedrós, A. GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis. bioRxiv 2023.12.05.570120. https://doi.org/10.1101/2023.12.05.570120

• pavianCore

  Florian P Breitwieser, Steven L Salzberg, Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification, Bioinformatics, Volume 36, Issue 4, February 2020, Pages 1303–1304, https://doi.org/10.1093/bioinformatics/btz715

External software/pipelines

• 10x Genomics Cell Ranger

  Zheng, G. X. Y. et al. (2017). Massively parallel digital transcriptional profiling of single cells. Nature Communications 8: 1-12, doi:10.1038/ncomms14049.

• BD Rhapsody™ Sequence Analysis Pipeline

  Becton, Dickinson and Company (2023). BD Rhapsody™ Sequence Analysis Pipeline: performs analysis of single-cell multiomic sequence read (FASTQ) data.

• Scale Bio SeqSuite

  ScaleBio (2023). ScaleBio Seq Suite: RNA Workflow.

• sci-rocket

  van Riet, J., Keegan, L. (2023). snakemake-scirocket: a Snakemake workflow which performs processing of sci-RNA-Seq3 data, including sample demultiplexing and downstream alignment and UMI-counting using STARSolo.

• split-pipe (Parse Biosciences Pipeline)

  Parse Biosciences Pipeline, Parse Biosciences, Seattle, USA; available at https://app.trailmaker.parsebiosciences.com

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.