Alternatives and similar repositories for hal

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

• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆187Updated last year
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆135Updated last year
• 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 2 months ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆171Updated last year
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆160Updated last week
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆106Updated 3 months ago
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆100Updated 3 weeks ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆159Updated 7 months ago
• marbl / ModDotPlot
  ☆161Updated last month
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆227Updated 9 months ago
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆195Updated last month
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆82Updated 3 years ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆104Updated 4 months ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆114Updated 4 months ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 4 years ago
• KolmogorovLab / Severus
  A tool for somatic structural variant calling using long reads
  ☆146Updated last week
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆98Updated 2 years ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆188Updated 4 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 2 months ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆101Updated last year
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆161Updated 3 years ago
• eldariont / svim
  Structural Variant Identification Method using Long Reads
  ☆175Updated 4 years ago
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆125Updated 2 months ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆158Updated 2 years ago
• PacificBiosciences / pb-assembly
  PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
  ☆118Updated 5 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆118Updated 5 months ago
• EVidenceModeler / EVidenceModeler
  source code for EVM
  ☆118Updated 10 months ago
• cgroza / GraffiTE
  GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered …
  ☆200Updated last week
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago