RASflow: an RNA-Seq analysis workflow with Snakemake by Xiaokang Zhang, Inge Jonassen

Subjects: Get full text

Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data by Hanna Sigeman, Bella Sinclair, Bengt Hansson

Subjects: Get full text

A Computational Approach to Demonstrate the Control of Gene Expression via Chromosomal Access in Colorectal Cancer by Caleb J. Pecka, Ishwor Thapa, Amar B. Singh, Dhundy Bastola

Subjects: Get full text

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes by Annabel Cansdale, James P. J. Chong

Subjects: Get full text

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2 by Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi, Kenji Mizuguchi

Subjects: “…snakemake…”
Get full text

Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing by Alicia Isabell Tüns, Till Hartmann, Simon Magin, Rocío Chamorro González, Rocío Chamorro González, Rocío Chamorro González, Rocío Chamorro González, Rocío Chamorro González, Anton George Henssen, Anton George Henssen, Anton George Henssen, Anton George Henssen, Anton George Henssen, Sven Rahmann, Alexander Schramm, Johannes Köster

Subjects: Get full text

ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications by Noah Herrick, Susan Walsh

Subjects: Get full text

SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes [version 2; peer review: 2 approved] by Vincent Hervé, Nachida Tadrent, Franck Dedeine

Subjects: “…Snakemake…”
Get full text

Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species by Daniel Fischer, Miika Tapio, Oliver Bitz, Terhi Iso-Touru, Antti Kause, Ilma Tapio

Subjects: Get full text

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] by Grant L. Hughes, Louise Cerdeira, Eva Heinz, Aidan Foo

Subjects: Get full text

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes by Amit Yadav, Srikrishna Subramanian

Subjects: Get full text

CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants by Jeremias Krause, Carlos Classen, Daniela Dey, Eva Lausberg, Luise Kessler, Thomas Eggermann, Ingo Kurth, Matthias Begemann, Florian Kraft

Subjects: Get full text

Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range by Megan A. Brenes Guallar, Like Fokkens, Like Fokkens, Martijn Rep, Lidija Berke, Peter van Dam

Subjects: Get full text

Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads by Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk, Daniela Beisser

Subjects: Get full text

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization by Lili Blumenberg, Kelly V. Ruggles

Subjects: Get full text

SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline [version 2; peer review: 2 approved] by John Krapohl, Brett E. Pickett

Subjects: Get full text

Association Mapping between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids by Maider Astorkia, Mónica Hernandez, Stéphanie Bocs, Emma Lopez de Armentia, Ana Herran, Kevin Ponce, Olga León, Shone Morales, Nathalie Quezada, Francisco Orellana, Fahmi Wendra, Zulhermana Sembiring, Dwi Asmono, Enrique Ritter

Subjects: Get full text

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

Subjects: Get full text

HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes by Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer, Ingo Hein

Subjects: Get full text