Alternatives and similar repositories for phyloFlash

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

• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆80Updated 2 years ago
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆65Updated 2 years ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆100Updated 3 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• AnantharamanLab / ViWrap
  A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
  ☆85Updated last year
• mdsufz / MuDoGeR
  MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
  ☆89Updated last year
• nylander / catfasta2phyml
  Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
  ☆75Updated last year
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆108Updated 4 years ago
• qichao1984 / NCyc
  ☆53Updated 5 years ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆114Updated 8 months ago
• KatariinaParnanen / MobileGeneticElementDatabase
  Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
  ☆52Updated 4 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆117Updated last year
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆49Updated 2 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆131Updated 4 months ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆47Updated 2 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆90Updated last month
• allind / EukDetect
  ☆56Updated 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…
  ☆82Updated 4 months ago
• treangenlab / emu
  ☆75Updated this week
• cmks / DAS_Tool
  DAS Tool
  ☆166Updated last year
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆93Updated last month
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆87Updated 2 years ago
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆62Updated 4 years ago
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆82Updated 8 months ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆61Updated last year
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆80Updated 7 months ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆57Updated 8 months ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆146Updated last week