Alternatives and similar repositories for svaha2

Users that are interested in svaha2 are comparing it to the libraries listed below

• edawson / svaha
  Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
  ☆11Updated last year
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆26Updated last year
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 4 years ago
• mchaisso / mcutils
  ☆12Updated 5 months ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 2 months ago
• fritzsedlazeck / SURVIVOR_ant
  A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
  ☆13Updated 7 years ago
• Parsoa / Nebula
  Ultra-efficient mapping-free structural variation genotyper
  ☆20Updated 4 years ago
• jts / mbtools
  ☆14Updated 2 years ago
• edawson / mkmh
  Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
  ☆24Updated 5 years ago
• bede / kindel
  Indel-aware consensus for aligned BAM
  ☆21Updated 5 months ago
• richarddurbin / syng
  syncmer graphs, and perhaps other sorts of sequence graphs
  ☆24Updated last month
• DecodeGenetics / LRcaller
  ☆16Updated 4 years ago
• VGP / vgp-tools
  ☆28Updated 10 months ago
• jmonlong / sveval
  Functions to compare a SV call sets against a truth set.
  ☆30Updated 7 months ago
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated this week
• collaborativebioinformatics / GeneVar
  ☆12Updated 4 years ago
• walaj / svlib
  Toolkit for extracting SVs from long sequences and benchmarking variant callers
  ☆13Updated 9 years ago
• DecodeGenetics / read_haps
  Detects human contamination in bam files
  ☆16Updated 5 years ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• mskilab-org / pgv
  Pan gGnome Viewer
  ☆10Updated 7 months ago
• jbelyeu / unfazed
  Unfazed by genomic variant phasing
  ☆27Updated last year
• lh3 / gfa1
  This repo is deprecated. Please use gfatools instead.
  ☆15Updated 7 years ago
• BrendelGroup / AEGeAn
  Integrated toolkit for analysis and evaluation of annotated genomes
  ☆25Updated 6 months ago
• kcleal / svbench
  Benchmark structural variant calls against a reference set
  ☆18Updated 2 weeks ago
• karel-brinda / samsift
  SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  ☆23Updated 4 months ago
• Gaius-Augustus / clamsa
  ClaMSA (Classify Multiple Sequence Alignments).
  ☆13Updated last year
• mklarqvist / djinn
  C++ library for analysing and storing large-scale cohorts of sequence variant data
  ☆17Updated 6 years ago
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆32Updated 4 years ago
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 9 months ago
• LankyCyril / edgecase
  A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, a…
  ☆16Updated 2 years ago