Does flye break raw reads?

mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs

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Does flye break raw reads? #145

Closed bbalog87 closed 5 years ago

bbalog87 commented 5 years ago

Hi Mikhail,

I have removed all raw reads shorter than 1kb. However the final polished flye assembly has contig shorter than 0.5kb. To my understanding of Flye algorithm, this shouldn't happen. Are some reads splitted in the consensus stage?

Best, Julien

mikolmogorov commented 5 years ago

Hi Julien,

Contigs are generated from repeat graph edges and could be as short as 0.5kb. Usually, unique contigs will be longer because they are extended into adjacent repeats using the read information. However, repetitive contigs (or perhaps plasmids / phages) can remain short.

Best, Mikhail