Alternatives and similar repositories for mashpit

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

• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated 2 weeks ago
• sourmash-bio / sourmash_plugin_branchwater
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆22Updated this week
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆56Updated last month
• PROBIC / mGEMS
  mGEMS Genomic epidemiology with mixed samples
  ☆16Updated 9 months ago
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated last year
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆23Updated 6 months ago
• jonas-fuchs / virHEAT
  Visualize microbial evolution at the SNP level!
  ☆14Updated 3 weeks ago
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆24Updated 6 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated last month
• Danderson123 / Amira
  A tool to detect acquired AMR genes directly from long read sequencing data.
  ☆15Updated last week
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 4 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
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• mbhall88 / psdm
  Compute a pairwise SNP distance matrix from one or two alignment(s)
  ☆25Updated 8 months ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 8 months ago
• ubinfie / ubinfie.github.io
  µbinfie blog
  ☆17Updated 2 months ago
• natir / rustyread
  A long read simulator based on badread idea
  ☆22Updated 2 years ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 weeks ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated last year
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆19Updated 4 months ago
• tlemane / kmdiff
  Differential k-mer analysis
  ☆36Updated last year
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated last month
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆24Updated 4 months ago
• mkirsche / Grafter
  Scaffolding with Ultralong Reads
  ☆15Updated 4 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• bacpop / pp-sketchlib
  Library of sketching functions used by PopPUNK
  ☆31Updated 2 months ago
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆33Updated last year