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
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆173Updated 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…
  ☆146Updated 3 months ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆228Updated 10 months ago
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆137Updated last year
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆160Updated 8 months ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆108Updated 4 months ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆162Updated 2 weeks ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆104Updated 4 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 4 years ago
• marbl / ModDotPlot
  ☆168Updated 2 weeks ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 3 months ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆160Updated 2 years ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆189Updated 5 months ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆101Updated last year
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆83Updated 3 years ago
• ComparativeGenomicsToolkit / Comparative-Annotation-Toolkit
  ☆181Updated 5 months ago
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆100Updated last month
• jtlovell / GENESPACE
  ☆218Updated 9 months ago
• lh3 / pangene
  Constructing a pangenome gene graph
  ☆196Updated 2 months ago
• PacificBiosciences / ccs
  CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
  ☆124Updated last year
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆115Updated 5 months ago
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆127Updated 3 months ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆117Updated 2 years ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 4 years ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆206Updated last year
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆172Updated 4 years ago
• HuiyangYu / PanDepth
  An ultra-fast and efficient genomic tool for coverage calculation
  ☆159Updated 7 months ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆234Updated 9 months ago