Alternatives and similar repositories for lofreq:

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

• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆111Updated last month
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆65Updated 3 months ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆88Updated 3 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆96Updated last year
• nanoporetech / wub
  Tools and software library developed by the ONT Applications group
  ☆62Updated 4 years ago
• Kingsford-Group / scallop
  Scallop is a reference-based transcriptome assembler for RNA-seq
  ☆89Updated 3 years ago
• epi2me-labs / wf-basecalling
  ☆35Updated 2 weeks ago
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆91Updated 4 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 8 months ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆97Updated 2 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆146Updated 3 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• nanoporetech / ont-assembly-polish
  ONT assembly and Illumina polishing pipeline
  ☆91Updated 4 years ago
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆86Updated 10 months ago
• rjchallis / assembly-stats
  Assembly statistic visualisation
  ☆89Updated last year
• ryanlayer / stix
  Structural Variant Index
  ☆71Updated 2 months ago
• milkschen / leviosam2
  Fast and accurate coordinate conversion between assemblies
  ☆112Updated 4 months ago
• nanoporetech / rerio
  Research release basecalling models and configurations
  ☆107Updated 7 months ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆104Updated 4 years ago
• parklab / bamsnap
  ☆119Updated 3 months ago
• CshlSiepelLab / phast
  PHAST
  ☆71Updated last month
• svviz / svviz
  Read visualizer for structural variants
  ☆81Updated 6 years ago
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆88Updated 2 months ago
• nanoporetech / qcat
  qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
  ☆78Updated 4 years ago
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆92Updated 8 years ago
• informationsea / transanno
  accurate LiftOver tool for new genome assemblies
  ☆119Updated 6 months ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 5 years ago
• GenomiqueENS / toulligQC
  A post sequencing QC tool for Oxford Nanopore sequencers
  ☆93Updated last month
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆132Updated 3 months ago