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DiltheyLab / MetaMaps

Long-read metagenomic analysis
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mapAgainstIndex #36

Closed Mattstorey closed 4 years ago

Mattstorey commented 4 years ago

Hi. Just wondering how and when to use the mapAgainstIndex and index commands? Thanks,

AlexanderDilthey commented 4 years ago

Hi @Mattstorey, This is how you could use the commands:

./mashmap index -r ref.fa -i myIndex1
./mashmap mapAgainstIndex -i myIndex1 -q test.fastq -o output

We don't recommend, however, using index-based mapping - it complicates the command line call scheme, and the benefits in terms out execution time are not particularly large.

Mattstorey commented 4 years ago

Thanks!