Alternatives and similar repositories for ccfind:

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

• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆17Updated last year
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 2 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• janka2012 / digIS
  Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes
  ☆9Updated 3 years ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆22Updated 5 months ago
• ablab / plasmidVerify
  plasmidVerify: plasmid contig verification tool
  ☆12Updated 4 years ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆11Updated 10 months ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆31Updated 3 months ago
• qiyunlab / binarena
  BinaRena: Interactive Visualization and Binning of Metagenomic Contigs
  ☆30Updated 4 months ago
• EnvGen / POGENOM
  Population genomics from metagenomes
  ☆11Updated 4 months ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated last year
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆14Updated last year
• jaumlrc / ProphET
  ☆10Updated 4 years ago
• valflanza / accnet
  ☆13Updated 7 years ago
• AlexanderLabWHOI / EukHeist
  ☆25Updated last year
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…
  ☆41Updated 3 weeks ago
• lgpdevtools / sraX
  Systematic resistome analysis
  ☆10Updated 4 years ago
• ewissel / hAMRoaster
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Updated 10 months ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 5 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆24Updated last month
• LottePronk / whokaryote
  Classify metagenomic contigs as eukaryotic or prokaryotic
  ☆32Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆20Updated 2 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 6 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆25Updated 2 months ago
• Arkadiy-Garber / MagicLamp
  A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
  ☆13Updated 6 months ago
• aweimann / traitar
  ☆22Updated last year
• metasnv-tool / metaSNV
  MetaSNV, a metagenomic SNV calling pipeline.
  ☆20Updated 2 years ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated last year
• lazzarigioele / graphanalyzer
  This is graphanalyzer.py, a script designed to automatically interpret the outputs generated by vConTACT2 when using the INPHARED databas…
  ☆18Updated last year
• gcremers / metascan
  Metabolic scanning and annotation of Metagenomes
  ☆10Updated 3 weeks ago