Alternatives and similar repositories for BAGEL4:

Users that are interested in BAGEL4 are comparing it to the libraries listed below

• zreitz / multismash
  A workflow and scripts for large-scale antiSMASH analyses
  ☆39Updated 2 weeks ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆40Updated 6 months ago
• michaelkyu / PlasX
  PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture
  ☆33Updated 3 years ago
• RasmussenLab / phamb
  Downstream processing of VAMB binning for Viral Elucidation
  ☆49Updated 9 months ago
• XiaofangJ / PhaseFinder
  A pipeline to computationally identify invertible DNA regions and quantify their orientations.
  ☆29Updated last year
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆58Updated last week
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆47Updated 2 months ago
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆56Updated last month
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆47Updated 2 months ago
• apcamargo / ictv-mmseqs2-protein-database
  ☆30Updated last month
• allind / EukDetect
  ☆50Updated last year
• ziyewang / MetaBinner
  ☆52Updated last year
• snayfach / UHGV
  Unified Human Gut Virome Catalog
  ☆28Updated 9 months ago
• EBI-Metagenomics / mettannotator
  ☆69Updated last month
• HubertTang / PLASMe
  ☆26Updated last year
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated last month
• 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 2 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated last year
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆61Updated 3 months ago
• samnooij / PathoFact
  Altered version of PathoFact to work more conveniently with SLURM and large input files
  ☆12Updated 5 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated 3 weeks ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆45Updated 2 weeks ago
• gatech-genemark / MetaGeneMark-2
  MetaGeneMark-2: Improved Gene Prediction in Metagenomes
  ☆21Updated last year
• Kalan-Lab / lsaBGC
  lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
  ☆37Updated 2 weeks ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated last year
• metagenopolis / CroCoDeEL
  CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
  ☆24Updated 2 weeks ago
• patrickwest / EukRep_Pipeline
  ☆24Updated 6 years ago
• Matteopaluh / KEMET
  KEGG Module Evaluation Tool
  ☆29Updated last year
• ablab / metaGT
  Pipeline for metagenome and metatranscriptome joint assembly
  ☆21Updated 2 years ago
• wandreopoulos / deeplasmid
  ☆20Updated 7 months ago