Alternatives and similar repositories for lemur

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

• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 9 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆52Updated 4 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated this week
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 10 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated 3 weeks ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆30Updated 2 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆65Updated 7 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆32Updated 2 weeks ago
• cruizperez / FastAAI
  ☆25Updated last year
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆32Updated 2 months ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆42Updated last year
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆34Updated 6 months ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• Dmitry-Antipov / viralFlye
  viralFlye pipeline
  ☆18Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 5 months ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆23Updated 6 months ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆50Updated 2 weeks ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 5 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 5 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆43Updated 5 years ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆39Updated 3 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆37Updated last year
• bluenote-1577 / fairy
  alignment-free coverage calculation for metagenomic binning >100 times faster
  ☆48Updated 10 months ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• bacpop / PopPIPE
  Population analysis PIPEline 🛠🧬
  ☆22Updated last week
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆29Updated 11 months ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆46Updated 10 months ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆27Updated 3 years ago