Alternatives and similar repositories for PhyloSift

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

• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆46Updated last year
• MadsAlbertsen / multi-metagenome
  Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
  ☆81Updated 9 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆54Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆55Updated last year
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆90Updated this week
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆103Updated 6 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆81Updated 3 months ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆56Updated 3 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆48Updated 3 years ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆47Updated 5 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆79Updated last month
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆56Updated 3 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆115Updated last year
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆74Updated last year
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 7 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 2 years ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆30Updated 5 years ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆73Updated last year
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆61Updated 2 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆116Updated last month