Faecal shotgun metagenomes of healthy stool donors from the Netherlands Donor Feces Bank and multiple recurrent Clostridioides difficile infection patients with long-term follow-up

A batch of faecal metagenomes of stool samples from multiple recurrent Clostridioides difficile infected patients collected before, shortly after and at a long-term after faecal microbiota transplantation, and stool samples of their respective donors. 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. The human read removal workflow is based on: https://git.lumc.nl/snooij/metagenomics-preprocessing