Alternatives and similar repositories for fast-lineage-caller

Users that are interested in fast-lineage-caller are comparing it to the libraries listed below

• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated last year
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 7 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆52Updated 5 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆27Updated 2 months ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆60Updated 2 weeks ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• CFIA-NCFAD / wgscovplot
  The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…
  ☆19Updated last year
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆15Updated 2 years ago
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 2 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆27Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 7 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆58Updated last year
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 9 months ago
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆43Updated 2 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 weeks ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 3 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 2 years ago
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 3 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 7 months ago
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated last year
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago