Alternatives and similar repositories for smartdenovo:

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

• xiaochuanle / NECAT
  Nanopore data assembler
  ☆147Updated 3 years ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆205Updated 2 years ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆220Updated 3 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆200Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 3 years ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆176Updated 5 months ago
• dfguan / purge_dups
  haplotypic duplication identification tool
  ☆233Updated last year
• BGI-Qingdao / TGS-GapCloser
  A gap-closing software tool that uses long reads to enhance genome assembly.
  ☆203Updated 7 months ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆179Updated last month
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆142Updated last month
• oushujun / LTR_retriever
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆199Updated 3 weeks ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆160Updated last year
• wdecoster / chopper
  ☆183Updated 3 weeks ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆184Updated 10 months ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆191Updated last month
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆178Updated last week
• marbl / ModDotPlot
  ☆142Updated 2 weeks ago
• huangnengCSU / compleasm
  A genome completeness evaluation tool based on miniprot
  ☆203Updated last month
• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆140Updated 5 months ago
• PacificBiosciences / ccs
  CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
  ☆119Updated last year
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆209Updated 3 months ago
• cgroza / GraffiTE
  GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered …
  ☆177Updated 2 weeks ago
• lh3 / gfatools
  Tools for manipulating sequence graphs in the GFA and rGFA formats
  ☆225Updated 8 months ago
• nanoporetech / modkit
  A bioinformatics tool for working with modified bases
  ☆185Updated this week
• Gabaldonlab / redundans
  Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
  ☆145Updated this week
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆149Updated 2 years ago
• xiaochuanle / MECAT
  MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
  ☆108Updated 4 years ago
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆170Updated 4 years ago
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆184Updated 2 weeks ago