epi2me-labs / wf-metagenomics

Related projects: ⓘ

• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated last year
• blobtoolkit / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆84Updated last month
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆94Updated this week
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 4 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆105Updated 10 months ago
• rhysf / Synima
  Synteny Imager
  ☆60Updated 3 weeks ago
• nadegeguiglielmoni / genome_assembly_tools
  List of genome assembly tools
  ☆44Updated 2 weeks ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆75Updated 2 years ago
• RemiAllio / MitoFinder
  MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
  ☆88Updated 5 months ago
• treangenlab / emu
  ☆31Updated 2 weeks ago
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆59Updated 9 months ago
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆52Updated this week
• rrwick / Metagenomics-Index-Correction
  ☆78Updated last year
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆94Updated 3 years ago
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆136Updated 2 weeks ago
• jamiemcg / BUSCO_phylogenomics
  BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
  ☆45Updated 7 months ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆67Updated 2 years ago
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆66Updated this week
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆31Updated 3 weeks ago
• CDCgov / mycosnp-nf
  CDCgov/mycosnp-nf
  ☆36Updated last week
• robotoD / GenoVi
  GenoVi, an automated customizable circular genome visualizer for bacteria and archaea
  ☆77Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 3 months ago
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆26Updated last year
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆105Updated 3 months ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆54Updated 5 months ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆47Updated 2 years ago
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆55Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆76Updated 3 weeks ago
• jhawkey / IS_mapper
  IS mapping software
  ☆50Updated 2 years ago