North Pond 2017 High Completion Bins

Assembled metagenomes from 2017 and metatranscriptomes from 2012, 2014, and 2017 cruises to North Pond (Mid-Atlantic Ridge) were prepared for binning with Binsanity (Graham et al., 2017) by building a bowtie index from each 150-kmer assembly using bowtie2-build (Langmead and Salzberg, 2012). Sequence alignment map (SAM) files were generated in bowtie from all the North Pond metagenomes (2012-2017) using each bowtie index file. The SAM files were then converted to a compressed binary version (BAM files). These BAM files and the assembled metagenomes and metatranscriptomes were run through Binsanity iteratively, a total of six times with a refinement step in between each binning and using checkm (Park et al., 2014) to identify high-completion bins. Low-completion and high-redundancy bins were combined after each binning step to be rebinned. Bins were classified using the following parameters:

1) High-completion: >90% complete with <10% redundancy, greater than 80% with <5% redundancy, or >50% with <2% redundancy

2) Low-completion: <50% complete with <5%redundancy

3) Strain heterogeneity: >90% complete with >90% strain heterogeneity

4) High-redundancy: >80% complete with >10% redundancy, or >50% complete >5% redundancy