Bastien
Chevreux
bach@chevreux.org

> Solomon Short

> ... .

# Parameters for special situations

## Introduction

Most of this chapter and many sections are just stubs at the moment.

## PacBio

### PacBio CCS reads

Declare the sequencing technology to be high-quality PacBio (PCBIOHQ). The last time I worked with CCS, the ends of the reads were not really clean, so using the proposed end clipping (which needs to be manually switched on for PCBIOHQ reads) may be advisable.

    ...
    parameters = PCBIOHQ_SETTINGS -CL:pec=yes
    ...

    readgroup
    technology=pcbiohq
    data=...
    ...

### PacBio error corrected reads

Declare the sequencing technology to be high-quality PacBio (PCBIOHQ). For self-corrected data or data corrected with other sequencing technologies, it is recommended to change the -CO:mrpg setting to a value which is 1/4th to 1/5th of the average coverage of the corrected PacBio reads across the genome. E.g.:

    ...
    parameters = PCBIOHQ_SETTINGS -CO:mrpg=5
    ...

    readgroup
    technology=pcbiohq
    data=...
    ...

for a project which has ~24x coverage. This necessity may change in later versions of MIRA though.