Config parameters suggestion about sequel II hifi reads and new species hifi reads

hattori-lab / SACRA

SACRA (Split Amplified Chimeric Read Algorithm) is the algorithm for correcting chimeric long-reads generated by MDA.

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Config parameters suggestion about sequel II hifi reads and new species hifi reads #11

Closed orctyr closed 2 years ago

orctyr commented 2 years ago

Hi Yuya,

SACRA is an excellent tool in my work. I had run successfully in example data and small data sets. I am a little confused that do I need to change the config.yaml in sequel II hifi reads (~15kb length && > 20Gb) ? And SACRA paper is focus on viral-meta sample, is there any difference to use SACRA when applying in MDA-treated single specie genome (like some species with ultra-low biomass or DNA)?

YuyaKiguchi commented 2 years ago

Hi,

Basically, the default parameters are applicable for hifi reads, but you can increase the alignment identity threshold of PARs and CARs of 75 to 85~95 for obtaining the more accurate alignment. Although SACRA was originally developed for phageome, theoretically it could also be applied to non-viral genomics. However, we have not validated adverse effects on the non-viral genomes, so please check the results carefully.

Yuya