How to skip Polishing step?

[chihminchang]

How to skip Polishing step?

[chihminchang]

One of ways is to rename the bwa and pilon in tools_opera_ms.
is there any other ways?

[TongChengxuan]

Hi Minchang,

An easy way is to give --no-polishing flag.

Example:
perl ../OPERA-MS.pl --contig-file contigs.fasta --short-read1 R1.fastq.gz --short-read2 R2.fastq.gz --long-read long_read.fastq --no-ref-clustering --no-polishing --out-dir testing

Best regards,
Chengxuan

[nnnagara]

The “--no-polishing” flag should do the trick. Niranjan From: chihminchang <[email protected]> Reply-To: CSB5/OPERA-MS <[email protected]> Date: Sunday, 26 July 2020 at 1:28 PM To: CSB5/OPERA-MS <[email protected]> Cc: Subscribed <[email protected]> Subject: [CSB5/OPERA-MS] How to skip Polishing step? (#46) How to skip Polishing step? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#46>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACNYPUCF4D4GKXAICUZL423R5O5GJANCNFSM4PHZ3RWA>. This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.