Alternatives and similar repositories for CoverM:

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

• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆283Updated last week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆319Updated 10 months ago
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆222Updated 2 years ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆241Updated 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…
  ☆208Updated this week
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆501Updated last year
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆307Updated 2 months ago
• jiarong / VirSorter2
  customizable pipeline to identify viral sequences from (meta)genomic data
  ☆247Updated 4 months ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆370Updated 7 months ago
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆295Updated last month
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆327Updated last year
• WrightonLabCSU / DRAM
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
  ☆277Updated 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…
  ☆400Updated 3 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆335Updated last year
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆362Updated this week
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆222Updated 2 years ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆334Updated this week
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆345Updated last month
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆210Updated this week
• biobakery / humann
  HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
  ☆193Updated 8 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆499Updated last month
• CAMI-challenge / CAMISIM
  CAMISIM: Simulating metagenomes and microbial communities
  ☆203Updated 8 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆241Updated last year
• ParBLiSS / FastANI
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆399Updated last year
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆404Updated last week
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆376Updated last week
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆222Updated 3 months ago
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆335Updated last week
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆357Updated 3 years ago