Host-cleaned DNA-seq of rectal swab samples from children in the MORDOR I study
Rectal samples were collected from children enrolled in the MORDOR I study in Niger and sequenced as described. Multiple human-sequence removal steps were performed: 1) Spliced Transcripts Alignment to a Reference (STAR) aligner removal of sequences that aligned to  the human reference genome 38 (hg38) and the Pantroglodytes genome (panTro4, 2011, UCSC). 2) Unaligned non-host reads quality-filtered (PriceSeqFilter with the -rnf 90 and -rqf 85 0.98 settings), subjected to duplicate removal, and compressed by cd-hit-dup (v4.6.1). Paired reads were then assessed for complexity by compression with the Lempel-Ziv-Welch algorithm. Read pairs with a compression space savings score lower than 0.45 were removed. 3) Another round of human reads removal was performed using the very-sensitive-local mode of Bowtie2 (v2.2.4) with the same hg38 and panTro4 reference genomes described above 39. 4) The remaining non-host read pairs were then passed onto Centrifuge (1.0.3) to align to the entire NCBI non-redundant collection that was downloaded on 2/28/2016. Any sequences marked by Centrifuge to belong to Chordates, plants, or Arthropods were removed. The remaining sequences were saved as fastq files with a dummy quality score of 40.