RapidAVA: All-vs-all overlap detection in HiFi reads (BIBM 2024)

Given a read file, output pairwise overlaps among all reads. Fast and memory-efficient.

Build

1. git clone
2. cd build
3. make all

Usage

Usage: ./rapidava [options]
Options:
  -overlaps    [int] Dump overlaps to file (0: no dump, 1: dump AG format, 2: load dumped overlaps, 3: dump PAF format, 4: dump PAF to /dev/shm <0>
  -k           [int] k value for minimizer <32>
  -threads     [int] Number of threads <1>
  -logfile     [string] Log file prefix <>
  -contigfile  [string] Contig file prefix <>
  -readfile    [string(s)] Read files (COMPULSORY)
  -acc         [double] Sequencing accuracy, similarity threshold for overlap detection & contig generation. <0.9850>
  -worstacc    [double] Worst accuracy threshold in overlap detection. <0.9700>
  -mmratio     [int] Minimizer ratio <193>
  -alignmm     [int] Minimum aligned minimizer threshold <3>
  -minmm       [int] Min count of minimizer, suggested value: depth / 10 <3>
  -maxmm       [int] Max count of minimizer, suggested value: 2.5 * depth <500>
  -chains      [int] Keep top x chains in minimizer seed-and-chain alignment <3>
  -overlap     [double] Min overlap bps ratio (0,1] in read overlapping of edge generation. <0.1000>
  -minedges    [int] Min support edges when extending reads in contig generation <2>
  -downsample  [int] Down-sample x% reads <100>
  -print       [int] Print debug info for this node id and its reverse complement. <-1>
  -ag          [string] Prefix of filename to output cleared assembly graph. Blank for no output. <>
  -gt          [string] Ground truth positions of nodes in reference, for debugging purpose only. <>