Alternatives and similar repositories for cgranges:

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

• marbl / MashMap
  A fast approximate aligner for long DNA sequences
  ☆279Updated 4 months ago
• pmelsted / bifrost
  Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
  ☆208Updated 10 months ago
• GFA-spec / GFA-spec
  Graphical Fragment Assembly (GFA) Format Specification
  ☆205Updated 6 months ago
• lh3 / ksw2
  Global alignment and alignment extension
  ☆130Updated last year
• thegenemyers / DALIGNER
  Find all significant local alignments between reads
  ☆140Updated 7 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆245Updated 8 months ago
• lh3 / minimap
  This repo is DEPRECATED. Please use minimap2, the successor of minimap.
  ☆105Updated 7 years ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆371Updated last year
• rvaser / spoa
  SIMD partial order alignment tool/library
  ☆164Updated last year
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆215Updated last week
• richarddurbin / pbwt
  Implementation of Positional Burrows-Wheeler Transform for genetic data
  ☆104Updated 3 weeks ago
• ekg / seqwish
  alignment to variation graph inducer
  ☆145Updated last week
• smarco / WFA-paper
  Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
  ☆200Updated 2 years ago
• yangao07 / abPOA
  abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
  ☆119Updated last week
• lh3 / gfatools
  Tools for manipulating sequence graphs in the GFA and rGFA formats
  ☆218Updated 6 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆240Updated 3 months ago
• dpryan79 / libBigWig
  A C library for handling bigWig files
  ☆75Updated last month
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆138Updated 6 months ago
• marbl / Winnowmap
  Long read / genome alignment software
  ☆274Updated 3 months ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆181Updated 2 months ago
• lh3 / kmer-cnt
  Code examples of fast and simple k-mer counters for tutorial purposes
  ☆167Updated 4 years ago
• COMBINE-lab / pufferfish
  An efficient index for the colored, compacted, de Bruijn graph
  ☆107Updated 4 months ago
• ksahlin / strobemers
  A repository for generating strobemers and evalaution
  ☆77Updated 10 months ago
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆206Updated last week
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆156Updated 2 years ago
• ChaissonLab / LRA
  Long read aligner
  ☆115Updated last year
• thegenemyers / FASTK
  A fast K-mer counter for high-fidelity shotgun datasets
  ☆123Updated last week
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆169Updated 8 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆198Updated 2 years ago
• ksahlin / strobealign
  Aligns short reads using dynamic seed size with strobemers
  ☆164Updated 2 weeks ago