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 this week
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated 2 months ago
• iqbal-lab-org / cobs
  COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
  ☆20Updated 9 months ago
• natir / rustyread
  A long read simulator based on badread idea
  ☆23Updated 2 years ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 7 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆53Updated 4 months ago
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆44Updated 2 years ago
• Danderson123 / Amira
  A tool to detect acquired AMR genes directly from long read sequencing data.
  ☆17Updated last month
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆59Updated this week
• tlemane / kmdiff
  Differential k-mer analysis
  ☆37Updated last year
• sourmash-bio / sourmash_plugin_branchwater
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆23Updated this week
• jonas-fuchs / virHEAT
  Visualize microbial evolution at the SNP level!
  ☆15Updated 3 weeks 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 11 months ago
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆25Updated 9 months ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 7 months ago
• rust-seq / minimizer-iter
  Iterate over minimizers of a DNA sequence
  ☆31Updated last year
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆37Updated last year
• 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
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated last month
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆19Updated 7 months ago
• sid-krish / rhometa
  metagenome population recombination rate estimation pipeline
  ☆12Updated last week
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated 2 years ago
• PROBIC / mSWEEP
  mSWEEP High-resolution sweep metagenomics using fast probabilistic inference
  ☆15Updated 10 months ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• bluenote-1577 / myloasm
  A new high-resolution long-read metagenome assembler for even noisy reads
  ☆79Updated last week
• c2-d2 / disty
  Disty McMatrixface - compute a distance matrix from a core genome alignment file
  ☆14Updated 2 years ago
• bacpop / pp-sketchlib
  Library of sketching functions used by PopPUNK
  ☆31Updated 5 months ago
• PROBIC / mGEMS
  mGEMS Genomic epidemiology with mixed samples
  ☆16Updated 11 months ago