Alternatives and similar repositories for 3d-dna

Users that are interested in 3d-dna are comparing it to the libraries listed below

• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆226Updated 5 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆215Updated 2 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆262Updated last month
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆284Updated last month
• jtlovell / GENESPACE
  ☆211Updated 5 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆308Updated 2 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆177Updated 8 months ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆388Updated last year
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆194Updated 2 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆257Updated 2 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆152Updated 2 years ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆291Updated 8 months ago
• HuiyangYu / PanDepth
  An ultra-fast and efficient genomic tool for coverage calculation
  ☆150Updated 3 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆203Updated last year
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆139Updated 3 years ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆258Updated 6 months ago
• wdecoster / chopper
  ☆198Updated 2 months ago
• ncbi / egapx
  Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
  ☆141Updated 3 weeks ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆185Updated last year
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆390Updated last month
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆138Updated 10 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆212Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆188Updated last year
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆216Updated 6 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆230Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• TobyBaril / EarlGrey
  Earl Grey: A fully automated TE curation and annotation pipeline
  ☆171Updated this week
• kcleal / gw
  Genome browser and variant annotation
  ☆310Updated last week
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago