Shotgun-sequenced raw reads were processed using SeqPrep (
https://github.com/jstjohn/SeqPrep) under default settings to merge overlapping paired-end reads and trim adaptors. Metagenomic assembly and binning were performed using the Aviary pipeline [
42]: pre-processed reads (post-SeqPrep) were first assembled with metaSPAdes [
43], then Minimap2 [
44] and Samtools [
45] were used to map sequences back to the assemblies and CoverM [
46] was used to generate coverage reports. Multiple tools were used in the binning step of Aviary pipeline, including CONCOCT [
47], VAMB [
48], MetaBAT [
49], MetaBAT2 [
50], MaxBin2 [
51], Rosella [
52] and DASTool [
53].
NCBI:
The bacterium SP_28H5_5 whole genome shotgun (WGS) project has the project accession BAAGKY000000000. This version of the project (01) has the accession number BAAGKY010000000, and consists of sequences BAAGKY010000001-BAAGKY010000077.