Alternatives and similar repositories for wf-metagenomics

Users that are interested in wf-metagenomics are comparing it to the libraries listed below

• GaetanBenoitDev / metaMDBG
  MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
  ☆181Updated 2 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆143Updated last year
• Gaius-Augustus / GALBA
  GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…
  ☆147Updated 9 months ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆148Updated last week
• nadegeguiglielmoni / genome_assembly_tools
  List of genome assembly tools
  ☆83Updated 2 weeks ago
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆114Updated 6 months ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆162Updated last month
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• rrwick / Perfect-bacterial-genome-tutorial
  ☆148Updated last year
• PacificBiosciences / pb-metagenomics-tools
  Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
  ☆195Updated 2 months ago
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆87Updated 4 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆144Updated 3 weeks ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆175Updated 2 years ago
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆113Updated last year
• artic-network / fieldbioinformatics
  The ARTIC fieldbioinformatics pipeline
  ☆125Updated last month
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆142Updated 2 years ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆117Updated 2 years ago
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆168Updated this week
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆106Updated 4 years ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆144Updated 2 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆116Updated last year
• wdecoster / nanostat
  Create statistic summary of an Oxford Nanopore read dataset
  ☆123Updated 3 years ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆178Updated 6 months ago
• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆205Updated last year
• art-egorov / lovis4u
  Bioinformatics tool for Locus Visualisation
  ☆143Updated 3 weeks ago
• cruizperez / MicrobeAnnotator
  Pipeline for metabolic annotation of microbial genomes
  ☆150Updated 7 months ago
• MaestSi / MetONTIIME
  A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
  ☆113Updated 7 months ago
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆85Updated 2 years ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆102Updated last year