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lpryszcz committed Jul 8, 2021
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Expand Up @@ -33,7 +33,8 @@ Running entire modPhred pipeline with live basecalling (~6 minutes using RTX2080
acc=PRJEB22772
~/src/modPhred/run -f ref/ECOLI.fa -o modPhred/$acc -i $acc/* -t4 --host ~/src/ont-guppy_3.6.1/bin/guppy_basecall_server
Note, you can enable automatic removal of intermediate files (FastQ/M) using ``--cleanup``.
Note, you can enable automatic removal of intermediate files (FastQ/M) using ``--cleanup``.

Instead you can run all steps one-by-one as follow:

.. code-block:: bash
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