Alternatives and similar repositories for ShigEiFinder

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

• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆15Updated 2 years ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 7 years ago
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 2 years ago
• appliedbinf / el_gato
  ☆10Updated 5 months ago
• katholt / AMRrules
  Organism-specific interpretation of AMR genotypes
  ☆14Updated last year
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆15Updated 2 years ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆60Updated 2 weeks ago
• jonas-fuchs / virHEAT
  Visualize microbial evolution at the SNP level!
  ☆15Updated last month
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆27Updated 2 months ago
• piyuranjan / SNIKT
  Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…
  ☆17Updated 2 years ago
• CFSAN-Biostatistics / bettercallsal
  Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
  ☆11Updated 2 months ago
• janka2012 / digIS
  Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes
  ☆11Updated 4 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 7 months ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated last year
• farhat-lab / fast-lineage-caller
  ☆14Updated 4 years ago
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆18Updated 7 months ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆31Updated 2 weeks ago
• 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
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated last month
• centre-pathogen-genomics / snippy-ng
  ☆20Updated last week
• Danderson123 / Amira
  A tool to detect acquired AMR genes directly from long read sequencing data.
  ☆17Updated last month
• rrwick / Are-reads-required
  ☆10Updated 3 months ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated 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
• genomic-medicine-sweden / TRANA
  A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
  ☆16Updated this week
• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆26Updated 3 weeks ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 9 months ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 7 months ago