From: Evaluating nanopore sequencing data processing pipelines for structural variation identification
Name | Type | Version | Release year | Threads | Language | Description | Citation |
---|---|---|---|---|---|---|---|
GraphMap | Aligner | 0.5.2 | 2016 | 16 | C++ | Aligns nanopore long reads with circular genome handling | [19] |
LAST | Aligner | 941 | 2011 | 16 | C++ | Modified BLAST, outputs MAF format | [20] |
minimap2 | Aligner | 2.1 | 2017 | 16 | C | Aligns error-prone long reads, faster and more accurate than BWA | [21] |
NGMLR | Aligner | 0.2.6 | 2017 | 16 | C++ | Works with nanopore long reads to generate high-quality SV calls | [22] |
NanoSV | SV caller | 1.2.0 | 2017 | 16 | Python | Identifies and clusters split reads based on genomic positions and orientations to identify breakpoint junctions of SVs | [23] |
Picky | SV caller | 0.2.a | 2017 | 16 | Perl | “Pick”-and-stitch segments from LAST alignments into representative alignments with a greedy algorithm | [24] |
Sniffles | SV caller | 1.0.8 | 2017 | 16 | C++ | Detects all types of SVs using split-read alignments, high-mismatch regions, and depth of coverage | [22] |