t 16

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Aligner. Version. Arguments used. Kart. 2.0.0. -t 16. BWA. 0.7.13. -t 16. Bowtie2. 2.2.9. -end-to-end –k 1 –p 16 –X 1000. Cushaw3. 3.0.2. -t 16 –multi 1.
TableS 1. Aligner version and arguments used in the evaluation Aligner

Version

Arguments used

Kart

2.0.0

-t 16

BWA

0.7.13

-t 16

Bowtie2

2.2.9

-end-to-end –k 1 –p 16 –X 1000

Cushaw3

3.0.2

-t 16 –multi 1

HPG-aligner

2.0.1

dna –report-best –paired-min-distance=0 – paired-max-distance=1000 –t 16

HISAT2

2.0.1

-k 1 –p 16 –X 1000 –no-spliced-alignment

Subread

1.5.0-p1

--SAMoutput -T 16 -M 10 -I 5 -d 100 -D 1000 -B 1 -t 1

BLASR

5.1

-sam –nproc 16 –bestn 1

LAST

828

-P16 | last-split

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