Alternatives and similar repositories for MeSS

Users that are interested in MeSS 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
  ☆45Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆28Updated 7 months ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆64Updated 2 years ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 10 months ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆61Updated last month
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆61Updated 10 months ago
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated 2 weeks ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 2 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆41Updated 5 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 4 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆55Updated last year
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• EBI-Metagenomics / mettannotator
  ☆72Updated last week
• achtman-lab / GrapeTree
  GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…
  ☆83Updated 7 months ago
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated last month
• compgenomicslab / TreeProfiler
  tree visualization for tree + annotation data
  ☆39Updated last month
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 2 months ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• cmkobel / CompareM2
  🦠📇 Microbial genomes-to-report pipeline
  ☆58Updated this week
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• xiaoli-dong / metaerg
  ☆41Updated 4 years ago
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆66Updated 4 months ago