Alternatives and similar repositories for treeWAS

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

• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated last year
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆128Updated last month
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆62Updated last year
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆147Updated this week
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆88Updated last month
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆56Updated last year
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆77Updated 4 months ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆116Updated 3 months ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆67Updated last year
• BenoitMorel / GeneRax
  ☆71Updated 3 weeks ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆38Updated 3 weeks ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆30Updated 5 years ago
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated last month
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 2 years ago
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆73Updated last year
• egonozer / in_silico_pcr
  Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.
  ☆47Updated 2 months ago
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆67Updated last month
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆121Updated 3 months ago
• MadsAlbertsen / multi-metagenome
  Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
  ☆81Updated 9 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 10 months ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated this week
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 6 months ago
• Zymo-Research / figaro
  An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
  ☆88Updated 11 months ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆161Updated last month
• agmcfarland / r_phylogenetics_worshop
  Using ggtree to build phylogenetic trees
  ☆47Updated 7 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 4 months ago