Alternatives and similar repositories for PATRIC-distribution

Users that are interested in PATRIC-distribution are comparing it to the libraries listed below

• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆49Updated this week
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆64Updated last week
• ParkinsonLab / MetaPro
  ☆22Updated 2 months ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆67Updated last year
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆60Updated 4 months ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆81Updated this week
• PedroMTQ / mantis
  A package to annotate protein sequences
  ☆60Updated 11 months ago
• enasequence / webin-cli
  Webin command line submission program.
  ☆38Updated 4 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆88Updated 3 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 9 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆33Updated last year
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆58Updated 4 years ago
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆88Updated 2 years ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆74Updated 2 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• AuReMe / emapper2gbk
  Convert GFF, fastas, annotation table and species name into Genbank.
  ☆17Updated 2 weeks ago
• bhattlab / phanta
  Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
  ☆71Updated 2 months ago
• apcamargo / taxopy
  A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers
  ☆52Updated last week
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆41Updated 2 years ago
• replikation / poreCov
  SARS-CoV-2 workflow for nanopore sequence data
  ☆42Updated last month
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 7 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆46Updated 2 years ago
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆27Updated 2 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆57Updated 9 months ago
• paulstothard / cgview
  CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
  ☆50Updated last year
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆58Updated 4 years ago
• hsinnan75 / GSAlign
  GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
  ☆60Updated last year
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated 3 months ago