Alternatives and similar repositories for shortbred

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

• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆44Updated last year
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆53Updated 5 years ago
• bhattlab / phanta
  Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
  ☆64Updated 2 months ago
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago
• ziyewang / MetaBinner
  ☆57Updated last year
• SegataLab / cmseq
  Set of utilities on sequences and BAM files
  ☆26Updated 3 years ago
• xiaoli-dong / metaerg
  ☆40Updated 4 years ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆44Updated last month
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 4 months ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆62Updated 2 months ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• ivlachos / agamemnon
  Accurate metagenomi/metatranscriptomic analysis pipeline
  ☆23Updated 4 years ago
• metaGmetapop / metapop
  A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
  ☆42Updated 2 years ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆64Updated last year
• Microbial-Ecology-Group / AMRplusplus
  AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…
  ☆39Updated this week
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆49Updated 3 weeks ago
• zjshi / snv_analysis_almeida2019
  ☆21Updated 5 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆32Updated this week
• TingtZHENG / VirMiner
  Scripts to quality control for metagenomic raw data, including removing the adapters, low quality reads, bases or PCR duplicates
  ☆18Updated 5 years ago
• victoriapascal / gutsmash
  gutSMASH
  ☆55Updated 9 months ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆45Updated 5 years ago
• pollardlab / MIDAS
  Metagenomic Intra-Species Diversity Analysis (MIDAS)
  ☆39Updated last year
• ohmeta / metapi
  A general metagenomics data mining system focus on robust microbiome research
  ☆58Updated last year
• lmlui / Jorg
  MAG Circularization Method
  ☆32Updated 3 years ago
• EBI-Metagenomics / mettannotator
  ☆75Updated this week
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆61Updated last year
• Matteopaluh / KEMET
  KEGG Module Evaluation Tool
  ☆31Updated last year
• allind / EukDetect
  ☆53Updated 2 months ago