Alternatives and similar repositories for CheckM

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

• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆350Updated 3 weeks ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆438Updated 2 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆361Updated last month
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆354Updated 3 years ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆351Updated last month
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆434Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆368Updated 3 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆331Updated last year
• jiarong / VirSorter2
  customizable pipeline to identify viral sequences from (meta)genomic data
  ☆263Updated 9 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆458Updated 9 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆363Updated last week
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆242Updated 2 years ago
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆307Updated 2 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆380Updated 3 weeks ago
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆422Updated 7 months ago
• ParBLiSS / FastANI
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆426Updated last month
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆369Updated last year
• labgem / PPanGGOLiN
  Build a partitioned pangenome graph from microbial genomes
  ☆276Updated this week
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆252Updated last year
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆264Updated 2 months ago
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆309Updated 5 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆544Updated last month
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆403Updated 3 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆361Updated 2 months ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆318Updated 6 months ago
• wwood / CoverM
  Read alignment statistics for metagenomics
  ☆364Updated this week
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆527Updated last year
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆219Updated last month
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆495Updated last week