Alternatives and similar repositories for pipelines

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

• EBI-Metagenomics / mettannotator
  ☆79Updated this week
• franciscozorrilla / SymbNET
  Teaching materials for SymbNET course: from MAGs to GEMs
  ☆14Updated last year
• mdsufz / MuDoGeR
  MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
  ☆88Updated last year
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆63Updated last month
• allind / EukDetect
  ☆54Updated 4 months ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆79Updated 2 years ago
• EBI-Metagenomics / EukCC
  Tool to estimate genome quality of microbial eukaryotes
  ☆38Updated 3 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.)
  ☆67Updated this week
• ziyewang / MetaBinner
  ☆59Updated last year
• medema-group / BiG-MAP
  ☆30Updated last month
• Gibbons-Lab / isb_course_2023
  Materials and presentation for the 2023 ISB Microbiome course.
  ☆24Updated last year
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 6 months ago
• ziyewang / COMEBin
  ☆62Updated last year
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆85Updated 6 months ago
• linxingchen / cobra
  A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…
  ☆80Updated 2 months ago
• Matteopaluh / KEMET
  KEGG Module Evaluation Tool
  ☆32Updated 2 years ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆44Updated 3 months ago
• AnantharamanLab / ViWrap
  A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
  ☆82Updated 10 months ago
• Gibbons-Lab / medi
  Metagenomic Estimation of Dietary Intake and Content.
  ☆33Updated 7 months ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• Carrion-lab / bacLIFE
  ☆50Updated last month
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆54Updated 5 years ago
• susiegriggo / Phynteny
  Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
  ☆55Updated 5 months ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆81Updated last month
• victoriapascal / gutsmash
  gutSMASH
  ☆56Updated last month
• patrickwest / EukRep_Pipeline
  ☆24Updated 6 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆62Updated 2 years ago
• ohlab / GRiD
  Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …
  ☆31Updated 5 years ago
• jolespin / veba
  A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metag…
  ☆96Updated last month