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Sequencing reads preparation and assembly

DA Davide Albanese
CC Claudia Coleine
OR Omar Rota-Stabelli
SO Silvano Onofri
ST Susannah G. Tringe
JS Jason E. Stajich
LS Laura Selbmann
CD Claudio Donati
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BBDuk (http://sourceforge.net/projects/bbmap/) v38.25 was used to remove contaminants, trim adapters, and low-quality sequences. The procedure removed reads that contained 4 or more “N” bases, had an average quality score across the read less than 3, or had a minimum length ≤ 51 bp or 33% of the full read length. Filtered and trimmed paired-end reads were error corrected using BFC [18] r181 with parameters -1 -s 10g -k 21 -t 10 and orphan reads were removed. Samples were assembled individually with SPAdes [19] 3.12.0 using the parameters -m 2000 -o spades3 --only-assembler -k 33,55,77,99,127 --meta -t 32.

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