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Table 1 Parameter settings and commands used by different methods for mapping of PacBio SMRT reads

From: S-conLSH: alignment-free gapped mapping of noisy long reads

Mapper

Command line settings

Minimap [15]

\({\texttt {/minimap -d in.mmi ref}}\_{\texttt {file}}\)

\({\texttt {./minimap -l in.mmi read}}\_{\texttt {file > output}}\_{\texttt {file}}\)

Minimap2 [7]

\({\texttt {./minimap2 -Hk19 -d in.mmi ref}}\_{\texttt {file}}\)

\({\texttt {./minimap2 -a -Y -x map-pb -t 1 in.mmi read}}\_{\texttt {file > output}}\_{\texttt {file}}\)

lordFAST [8]

\({\texttt {./lordfast --index ref}}\_{\texttt {file}}\)

\({\texttt {./lortfast --search ref}}\_{\texttt {file --seq read}}\_{\texttt {file --thread 1 > output}}\_{\texttt {file}}\)

MUMmer4 [10]

\({\texttt {./nucmer --sam-long=output}}\_{\texttt {file ref}}\_{\texttt {file read}}\_{\texttt {file -l 15 -c 31}}\)

conLSH [16]

\({\texttt {./conLSH-indexer}}\) \(\${\texttt {PATH ref}}\_{\texttt {file -K 2 -L 1 > output}}\_{\texttt {file}}\)

\({\texttt {./conLSH-aligner}}\) \(\${\texttt {PATH read}}\_{\texttt {file ref}}\_{\texttt {file -K 2 -L 1 -l 8 -w 1000 -m 5 --lambda 2 > output}}\_{\texttt {file}}\)

S-conLSH

\({\texttt {./S-conLSH}}\) \(\${\texttt {PATH ref}}\_{\texttt {file read}}\_{\texttt {file -K 2 --lambda 3 -L 2 -z 5 > output}}\_{\texttt {file}}\)