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