Metagenomic shotgun sequencing of healthy stool bank donors and multiple recurrent Clostridioides infected recipients from the Netherlands Donor Feces Bank. Fecal microbiota transplantation for Clostridioides difficile infection

Fecal shotgun metagenomes of healthy donors from the Netherlands Donor Feces bank and of multiple recurrent Clostridioides infected patients treated by fecal microbiota transplantation. Note that for privacy reasons, human-derived reads have been removed from these files by mapping raw reads to the human reference genome (GRCh38.p7 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.33/)) using bowtie2 (version 2.4.2) with the '--very-sensitive-local' parameter. Non-mapping reads are selected with samtools (version 1.11) using the parameters ' -f 1 -f 4 -f 8'. The resulting paired-end raw read files are deposited here. This publication first described the dataset: https://doi.org/10.1053/j.gastro.2021.06.009 The human read removal workflow is based on: https://git.lumc.nl/snooij/metagenomics-preprocessing