Alternatives and similar repositories for metagenomics:

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

• SegataLab / metamlst
  MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
  ☆15Updated 2 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆44Updated 4 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 9 months ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 4 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
  ☆57Updated 7 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆48Updated 2 years ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆36Updated 6 months ago
• CAMI-challenge / OPAL
  OPAL: Open-community Profiling Assessment tooL
  ☆28Updated 3 months ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆64Updated 5 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated this week
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆44Updated 8 months ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 9 months ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• WatsonLab / KOunt
  Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.
  ☆24Updated 6 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆93Updated 7 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆59Updated last week
• jonas-fuchs / SARS-CoV-2-analyses
  Collection of R scripts for SARS-CoV-2 (variant) analyses
  ☆12Updated 2 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 3 months ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆62Updated 2 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• naturalis / wgs2ncbi
  Toolkit for preparing genomes for submission to NCBI
  ☆29Updated 3 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆39Updated 5 months ago
• katholt / RedDog
  ☆36Updated 3 years ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆60Updated 2 years ago
• EBI-Metagenomics / mettannotator
  ☆69Updated last month