Alternatives and similar repositories for SneakerNet:

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

• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 3 months ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated last year
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 7 months ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated last month
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• klebgenomics / Kleborate-viz
  Visualisation application for Klebsiella genotypes generated by Kleborate.
  ☆9Updated 3 years ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆24Updated 9 months ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆24Updated 2 months ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• B-UMMI / INNUca
  INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
  ☆14Updated 2 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆34Updated 3 months ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆11Updated 10 months ago
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated 7 months ago
• LuoGroup2023 / PanTax
  Strain-level taxonomic classification of metagenomic data using pangenome graphs
  ☆22Updated 2 months ago
• farhat-lab / fast-lineage-caller
  ☆13Updated 3 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated last week
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated last year
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆26Updated 2 years ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆22Updated 9 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 months ago
• nodrogluap / nanostripper
  Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
  ☆14Updated 3 years ago
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆14Updated last year
• piyuranjan / SNIKT
  Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…
  ☆16Updated last year
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 5 years ago
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆20Updated last year