395 skills found · Page 1 of 14
rrwick / Unicyclerhybrid assembly pipeline for bacterial genomes
oschwengers / BaktaRapid & standardized annotation of bacterial genomes, MAGs & plasmids
Ecogenomics / GTDBTkGTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
bactopia / BactopiaA flexible pipeline for complete analysis of bacterial genomes
ncbi / AmrAMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
rrwick / TrycyclerA tool for generating consensus long-read assemblies for bacterial genomes
tseemann / Barrnap:microscope: :leo: Bacterial ribosomal RNA predictor
tseemann / Shovill⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
assemblerflow / FlowcraftFlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:
rrwick / AutocyclerA tool for generating consensus long-read assemblies for bacterial genomes
nickjcroucher / GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
jotech / GapseqInformed prediction and analysis of bacterial metabolic pathways and genome-scale networks
rrwick / Long Read Assembler ComparisonBenchmarking of long-read assembly tools for bacterial whole genomes
rrwick / Perfect Bacterial Genome TutorialNo description available
marbl / ParsnpParsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
gbouras13 / HybracterAutomated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
katholt / Srst2Short Read Sequence Typing for Bacterial Pathogens
jameshadfield / Phandangoan interactive viewer for populations of bacterial genomes linked by a phylogeny
rpetit3 / Dragonflye:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
bhattlab / MGEfinderA toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
