Alternatives and similar repositories for MashMap

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

• marbl / Winnowmap
  Long read / genome alignment software
  ☆310Updated last month
• lh3 / gfatools
  Tools for manipulating sequence graphs in the GFA and rGFA formats
  ☆248Updated last month
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆239Updated 7 months ago
• GFA-spec / GFA-spec
  Graphical Fragment Assembly (GFA) Format Specification
  ☆218Updated last year
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆307Updated last year
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆213Updated 3 years ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆226Updated 11 months ago
• lbcb-sci / racon
  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
  ☆234Updated 2 years ago
• rvaser / spoa
  SIMD partial order alignment tool/library
  ☆171Updated 4 months ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆284Updated last year
• Benson-Genomics-Lab / TRF
  Tandem Repeats Finder: a program to analyze DNA sequences
  ☆198Updated 3 years ago
• fbreitwieser / krakenuniq
  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
  ☆243Updated 2 years ago
• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆326Updated 4 months ago
• thegenemyers / FASTGA
  Pairwise whole genome aligner
  ☆225Updated 2 weeks ago
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆170Updated 4 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆270Updated 7 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆263Updated last year
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆210Updated last week
• ruanjue / smartdenovo
  Ultra-fast de novo assembler using long noisy reads
  ☆136Updated 4 years ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆285Updated 5 months ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆207Updated 3 years ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆162Updated 11 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 4 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆285Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆290Updated last month
• marbl / merqury
  k-mer based assembly evaluation
  ☆334Updated last year
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆240Updated last year
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆278Updated 2 years ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆188Updated last year
• isovic / graphmap
  GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…
  ☆182Updated 6 years ago