Alternatives and similar repositories for lofreq

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

• nanoporetech / wub
  Tools and software library developed by the ONT Applications group
  ☆64Updated 4 years ago
• fbreitwieser / bamcov
  Quickly calculate and visualize sequence coverage in alignment files
  ☆101Updated 6 years ago
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆92Updated 5 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆120Updated last month
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated 3 months ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• SorenKarst / longread_umi
  ☆80Updated 5 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆107Updated 4 years ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆112Updated 2 months ago
• nanoporetech / qcat
  qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
  ☆81Updated 4 years ago
• glennhickey / progressiveCactus
  Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
  ☆88Updated 7 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆73Updated 9 years ago
• GenomiqueENS / toulligQC
  A post sequencing QC tool for Oxford Nanopore sequencers
  ☆103Updated 4 months ago
• cbg-ethz / shorah
  Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
  ☆41Updated 2 years ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 6 months ago
• parklab / bamsnap
  ☆123Updated 4 months ago
• bcgsc / biobloom
  Create Bloom filters for a given reference and then use it to categorize sequences
  ☆76Updated last year
• lh3 / unimap
  A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
  ☆87Updated 4 years ago
• nanoporetech / ont-assembly-polish
  ONT assembly and Illumina polishing pipeline
  ☆89Updated 4 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago
• chiulab / surpi
  SURPI
  ☆86Updated 9 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated 2 years ago
• relipmoc / skewer
  ☆96Updated 3 years ago
• cpockrandt / genmap
  GenMap - Fast and Exact Computation of Genome Mappability
  ☆113Updated last year
• mw55309 / Kraken_db_install_scripts
  Updated Kraken DB install scripts to cope with new-ish NCBI structure
  ☆48Updated 8 years ago
• ryanlayer / stix
  Structural Variant Index
  ☆75Updated 11 months ago
• genotoul-bioinfo / dgenies
  Dotplot large Genomes in an Interactive, Efficient and Simple way
  ☆108Updated last month
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆131Updated last month
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆83Updated 3 years ago