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Tychus: a whole genome sequencing pipeline for assembly, annotation and phylogenetics of bacterial genomes

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.foodcont.2015.05.017openalex-snapshot

A modeling framework to accelerate food-borne outbreak investigations

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btr509openalex-snapshot

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot

ABySS: A parallel assembler for short read sequence data

inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

inferredcites →https://doi.org/10.1371/journal.pone.0060843openalex-snapshot

CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes

inferredcites →https://doi.org/10.3201/eid2208.151917openalex-snapshot

Whole-Genome Sequencing Detection of OngoingListeriaContamination at a Restaurant, Rhode Island, USA, 2014

inferredcites →https://doi.org/10.6084/m9.figshare.1254958openalex-snapshot

A novel tool for highly scalable computational pipelines

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s00284-020-01905-8openalex-snapshot

First Report of Isolation and Genome Sequence of L. petauri Strain from a Rainbow Trout Lactococcosis Outbreak

inferred← citeshttps://doi.org/10.1016/j.fsi.2022.03.028openalex-snapshot

Listeria monocytogenes isolates from Cornu aspersum snails: Whole genome-based characterization and host-pathogen interactions in a snail infection model

inferred← citeshttps://doi.org/10.1093/jacamr/dlad089openalex-snapshot

The genomic characterization of carbapenem-resistant Serratia marcescens at a tertiary hospital in South Africa

inferred← citeshttps://doi.org/10.1101/2024.04.09.588649openalex-snapshot

Whole genome sequencing and comparative genomic studies of Priestia filamentosa JURBA-X for its drought-tolerance, plant-growth promotion, and fluorescent characteristics

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