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Table 2 Evaluated aligners and SV callers

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]