Alternatives and similar repositories for CCMetagen

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

• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 2 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆78Updated last month
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆61Updated 3 weeks ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆49Updated 5 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆33Updated 5 years 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
• bobeobibo / phigaro
  Phigaro is a scalable command-line tool for predicting phages and prophages
  ☆52Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆45Updated last month
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆53Updated 5 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆54Updated 11 months ago
• voorloopnul / awesome-phages
  A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
  ☆50Updated 3 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• ziyewang / COMEBin
  ☆55Updated last year
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆71Updated 3 years ago
• EBI-Metagenomics / mettannotator
  ☆72Updated this week
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated last year
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆61Updated 2 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆59Updated last year
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆44Updated last year
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆42Updated last week
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆70Updated 3 weeks ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆85Updated 2 months ago