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Table 2 Evaluated aligners and SV callers

From: Evaluating nanopore sequencing data processing pipelines for structural variation identification

NameTypeVersionRelease yearThreadsLanguageDescriptionCitation
GraphMapAligner0.5.2201616C++Aligns nanopore long reads with circular genome handling[19]
LASTAligner941201116C++Modified BLAST, outputs MAF format[20]
minimap2Aligner2.1201716CAligns error-prone long reads, faster and more accurate than BWA[21]
NGMLRAligner0.2.6201716C++Works with nanopore long reads to generate high-quality SV calls[22]
NanoSVSV caller1.2.0201716PythonIdentifies and clusters split reads based on genomic positions and orientations to identify breakpoint junctions of SVs[23]
PickySV caller0.2.a201716Perl“Pick”-and-stitch segments from LAST alignments into representative alignments with a greedy algorithm[24]
SnifflesSV caller1.0.8201716C++Detects all types of SVs using split-read alignments, high-mismatch regions, and depth of coverage[22]