Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species

Authors: Daniel Fischer, Miika Tapio, Oliver Bitz, Terhi Iso-Touru, Antti Kause, Ilma Tapio

Source: BMC Genomics, Vol 26, Iss 1, Pp 1-17 (2025)

Subject Terms: Genotyping by sequencing, Snakemake, Variant calling, Cattle, Aquaculture, Repeatability, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

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CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants

Authors: Jeremias Krause, Carlos Classen, Daniela Dey, Eva Lausberg, Luise Kessler, Thomas Eggermann, Ingo Kurth, Matthias Begemann, Florian Kraft

Source: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-11 (2024)

Subject Terms: CNV, NGS, CNVkit, AnnotSV, Snakemake, Long-read sequencing, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/8817d02644c646b581b25199d78baa15

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes

Authors: Amit Yadav, Srikrishna Subramanian

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-15 (2024)

Subject Terms: Metagenome, PacBio HiFi technology, BGC, Workflow, Snakemake, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/15600ea1715842b783bab5e72771b9d1

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes

Authors: Annabel Cansdale, James P. J. Chong

Source: Microbiome, Vol 12, Iss 1, Pp 1-10 (2024)

Subject Terms: Metagenomics, Snakemake, Bioinformatics, Pipeline, MAGs, Microbiome, Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2049-2618

Access URL: https://doaj.org/article/aa2449fa5e364317a84db4aec5b41211

A Computational Approach to Demonstrate the Control of Gene Expression via Chromosomal Access in Colorectal Cancer

Authors: Caleb J. Pecka, Ishwor Thapa, Amar B. Singh, Dhundy Bastola

Source: BioMedInformatics, Vol 4, Iss 3, Pp 1822-1834 (2024)

Subject Terms: colorectal cancer, epigenetics, chromatin accessibility, snakemake, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://www.mdpi.com/2673-7426/4/3/100; https://doaj.org/toc/2673-7426

Access URL: https://doaj.org/article/7d88edf90f47413baa49811187c629b3

ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications

Authors: Noah Herrick, Susan Walsh

Source: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-18 (2023)

Subject Terms: Genomics, Genetic data, Pipeline, Snakemake, Workflow, Genome mapping, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/af6a4e1476424a919b01a9d3252f7fc3

HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes

Authors: Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer, Ingo Hein

Source: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-10 (2023)

Subject Terms: SMRT-AgRenSeq-d, dRenSeq, HiFi sequencing, Snakemake, High-throughput, Plant disease resistance, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/c7d21a50de1541a7bbd43aad155285e3

Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data

Authors: Hanna Sigeman, Bella Sinclair, Bengt Hansson

Source: BMC Genomics, Vol 23, Iss 1, Pp 1-14 (2022)

Subject Terms: Sex chromosomes, Snakemake, Paired-end, Genomics, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/339721e9297e4e12a5d407c3853ae7ea

Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR [version 2; peer review: 1 approved, 2 approved with reservations]

Authors: Grant L. Hughes, Louise Cerdeira, Eva Heinz, Aidan Foo

Source: Wellcome Open Research, Vol 8 (2023)

Subject Terms: Mosquito, Aedes aegypti, Microbiome, Metagenomics, Snakemake, MAGs, eng, Medicine, Science

File Description: electronic resource

Relation: https://wellcomeopenresearch.org/articles/8-131/v2; https://doaj.org/toc/2398-502X

Access URL: https://doaj.org/article/f7b3053047af40d1acf387f1c8530612

GRAPE: genomic relatedness detection pipeline [version 2; peer review: 2 approved]

Authors: Pavel Nikonorov, Dmitry Kolobkov, Hui Wang, Ruslan Vakhitov, Vitalina Chamberlain-Evans, Dmitriy Osipenko, Mikhail Kosaretskiy, Egor Kosaretskiy, Alexander Tischenko, Alexander Medvedev, Andrew Ponomarev, Mikhail Lebedev

Source: F1000Research, Vol 11 (2023)

Subject Terms: kinship and relationship estimation, identity-by-descent, snakemake workflow, bioinformatics pipeline, phasing and imputation, sequencing data, eng, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/11-589/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/0fe1fca846e740938b643ca4e0d9ffc9

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes [version 2; peer review: 2 approved]

Authors: Vincent Hervé, Nachida Tadrent, Franck Dedeine

Source: F1000Research, Vol 11 (2023)

Subject Terms: Snakemake, metagenomics, microbiology, genomics, bioinformatics, microbial ecology, eng, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/11-1522/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/b06bb4cbcd0049bd95caef8cdd1f3e12

Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range

Authors: Megan A. Brenes Guallar, Like Fokkens, Martijn Rep, Lidija Berke, Peter van Dam

Source: Frontiers in Plant Science, Vol 13 (2022)

Subject Terms: effectors, mimp, effector prediction, host specificity, snakemake, SIX genes, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpls.2022.1012688/full; https://doaj.org/toc/1664-462X

Access URL: https://doaj.org/article/f44fed162a004e289c5ac3a13440c70f

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

Authors: Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Mark D. Robinson

Source: BMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021)

Subject Terms: Snakemake, Epigenetics, Bisulfite-sequencing, Polyploidy, Allopolyploids, Reproducibility, Biotechnology, TP248.13-248.65, Genetics, QH426-470

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Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/57db0961d7e8412db51573fefefac1bb

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2

Authors: Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi

Source: Frontiers in Bioinformatics, Vol 2 (2022)

Subject Terms: snakemake, QIIME2, microbiome, 16S, automation, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fbinf.2022.893933/full; https://doaj.org/toc/2673-7647

Access URL: https://doaj.org/article/ca02dad871fc4ee993941b8dfda2fee5

Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

Authors: Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk, Daniela Beisser

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-14 (2020)

Subject Terms: Amplicon sequencing, Operational Taxonomic Units, Amplicon Sequence Variants, Snakemake, Pipline, Illumina, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-03852-4; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/5c83108527fa426e9d3e97b719d37240

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization

Authors: Lili Blumenberg, Kelly V. Ruggles

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-7 (2020)

Subject Terms: Machine learning, Unsupervised clustering, Hyperparameter optimization, Scikit-learn, Python, SnakeMake, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: http://link.springer.com/article/10.1186/s12859-020-03774-1; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/bf74a289c7ec4892a6b2a074758bde05

Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing

Authors: Alicia Isabell Tüns, Till Hartmann, Simon Magin, Rocío Chamorro González, Anton George Henssen, Sven Rahmann, Alexander Schramm, Johannes Köster

Source: Frontiers in Genetics, Vol 13 (2022)

Subject Terms: cancer, circular DNA, nanopore sequencing, algorithm, snakemake, Genetics, QH426-470

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Relation: https://www.frontiersin.org/articles/10.3389/fgene.2022.867018/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/66e0271a213b461695eace0945899692

SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline [version 2; peer review: 2 approved]

Authors: John Krapohl, Brett E. Pickett

Source: F1000Research, Vol 11 (2022)

Subject Terms: metaWRAP, shotgun metagenomics, high-performance computing, big data, Snakemake, eng, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/11-265/v2; https://doaj.org/toc/2046-1402

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RASflow: an RNA-Seq analysis workflow with Snakemake

Authors: Xiaokang Zhang, Inge Jonassen

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-9 (2020)

Subject Terms: RNA-Seq, Workflow, Snakemake, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-3433-x; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/ff7ff3d95cb4415c92736a8606773366

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Authors: MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018)

Subject Terms: RNA-seq, Analysis, Pipeline, Snakemake, Gene fusion, Immunological infiltrate, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

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Relation: http://link.springer.com/article/10.1186/s12859-018-2139-9; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/05f5ce1145074e0bbe0ea6794782fc82