hybrid assembly: POLCA polishing

hoelzer / mgnify-lr

Evaluation of long-read support for the MGnify pipeline

GNU General Public License v3.0

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Closed hoelzer closed 4 years ago

hoelzer commented 4 years ago

hoelzer commented 4 years ago

For now it seemst the most simple way to implement this using metaSPAdes with --nanopore parameter in the currently present CWL scripts.

hoelzer commented 4 years ago

POLCA is part of masurca:

masurca-polish.sh -a -r <'Illumina_reads_fastq1 Illumina_reads_fastq'> -t [-n] <optional:do not fix errors that are found>

hoelzer commented 4 years ago

PILON is used