Alternatives and similar repositories for metagenomics

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

• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 5 months ago
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆59Updated 2 months ago
• 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
• deng-lab / viroprofiler
  A containerized bioinformatics pipeline for viral metagenomic data analysis
  ☆37Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆34Updated 11 months ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆54Updated last month
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• pollardlab / MIDAS
  Metagenomic Intra-Species Diversity Analysis (MIDAS)
  ☆40Updated last year
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆72Updated 3 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆68Updated 3 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆32Updated last year
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆52Updated 3 weeks ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆70Updated 3 weeks ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated last month
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last month
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆66Updated last year
• xiaoli-dong / metaerg
  ☆40Updated 4 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 5 years ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆45Updated 4 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆96Updated 2 months ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• compgenomicslab / TreeProfiler
  tree visualization for tree + annotation data
  ☆44Updated 5 months ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆62Updated 5 months ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆48Updated 2 weeks ago
• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆49Updated 2 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆66Updated 3 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 2 months ago