Alternatives and similar repositories for fargene:

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

• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆44Updated last year
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆52Updated 9 months ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆44Updated 3 weeks ago
• Shamir-Lab / SCAPP
  SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…
  ☆31Updated last year
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆70Updated 5 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆26Updated 2 weeks ago
• guyleonard / taxdump_edit
  Add new taxa or taxonomic groups to the NCBI Taxdump files
  ☆19Updated 4 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated 3 weeks ago
• AuReMe / emapper2gbk
  Convert GFF, fastas, annotation table and species name into Genbank.
  ☆14Updated 10 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆38Updated 4 months ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated last year
• RasmussenLab / phamb
  Downstream processing of VAMB binning for Viral Elucidation
  ☆48Updated 7 months ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆51Updated 4 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• EBI-Metagenomics / EukCC
  Tool to estimate genome quality of microbial eukaryotes
  ☆36Updated 3 weeks ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• XiaofangJ / PhaseFinder
  A pipeline to computationally identify invertible DNA regions and quantify their orientations.
  ☆29Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• ziyewang / MetaBinner
  ☆50Updated 11 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆53Updated last week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 10 months ago
• marbl / harvest
  ☆52Updated 3 years ago
• patrickwest / EukRep_Pipeline
  ☆24Updated 6 years ago