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Remove mention of lastdb -P because it does not impact the alignment …
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charles-plessy committed Aug 8, 2024
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Expand Up @@ -47,12 +47,6 @@ Please see the [parameter documentation](https://nf-co.re/pairgenomealign/parame

- The `last-train` commands runs with `--revsym` as the DNA strands play equivalent roles in the studied genomes.

- The `lastdb` command takes all CPU cores available (`lastdb -P0`). Note that
when using more than one core, the output of `lastdb` may vary, causing the
order of tied positions to change. To prevent this to happen, you can pass a
nextflow parameter file to the pipeline that reduces the number of CPUs
allocated to `LAST_LASTDB` to 1.

## Running the pipeline

The typical command for running the pipeline is as follows:
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