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BioGEOTRACES comparisons

SK Sean M. Kearney
ET Elaina Thomas
AC Allison Coe
SC Sallie W. Chisholm
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PhyloFlash v3.0 (https://github.com/HRGV/phyloFlash) [84] was used to obtain SSU rRNA reads mapping to the 16S genes in bioGEOTRACES metagenomes [63] and low complexity reads were removed using komplexity v0.3.6 (https://github.com/eclarke/komplexity). Bacterial reads were obtained using bbsplit v38.22 (https://sourceforge.net/projects/bbmap/) with curated databases (https://osf.io/e65rs/) from SILVA 132 and aligned to group-specific references using PyNAST v1.2.2 [85]. Custom scripts were then used to obtain metagenomic reads mapping to the primer region for the 515Y/926R primer pair, and were followed by low-complexity masking and quality filtering all courtesy of Jesse McNichol (data and code can be found at https://osf.io/n5ftw/, and the full workflow at https://github.com/jcmcnch/MGPrimerEval). The final fastqs containing metagenomic reads mapping to the 515Y/926R region were used as input for downstream analysis. These bioGEOTRACES reads and the culture ASVs were imported into QIIME 2 [74] through which the sequences were dereplicated and clustered at 97% identity with VSEARCH [75]. The OTUs were then assigned taxonomies using the gg-13-8-99-nb-classifier [76, 77] and represented on maps using the accompanying bioGEOTRACES metadata.

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