Alternatives and similar repositories for KAT

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

• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆188Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆174Updated 4 years ago
• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆145Updated 5 months ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆207Updated 3 years ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆208Updated 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…
  ☆306Updated last year
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆238Updated 11 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 4 years ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆209Updated 2 years ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆217Updated 2 years ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆143Updated 4 months ago
• Gabaldonlab / redundans
  Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
  ☆163Updated 7 months ago
• ruanjue / smartdenovo
  Ultra-fast de novo assembler using long noisy reads
  ☆135Updated 4 years ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆173Updated 3 months ago
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆172Updated 4 years ago
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆122Updated last year
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆119Updated 2 years ago
• PASApipeline / PASApipeline
  PASA software
  ☆197Updated 9 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
• lh3 / gfatools
  Tools for manipulating sequence graphs in the GFA and rGFA formats
  ☆242Updated last year
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆227Updated 4 months ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆145Updated this week
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆177Updated 2 years ago
• chrishah / MITObim
  MITObim - mitochondrial baiting and iterative mapping
  ☆114Updated 4 years ago
• wdecoster / chopper
  ☆220Updated last week
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆190Updated 7 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆210Updated last year
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆216Updated last year
• oushujun / LTR_retriever
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆214Updated 5 months ago