REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited Data
BAM files containing sequencing data from crypts isolated from IBD patients.	This paper.	European Genome-phenome Archive (EGA) - accession code EGA: EGAD00001006061
Images of microdissections and physical distances between crypts.	This paper.	Mendeley Data: https://doi.org/10.17632/x3vsxpspn4.2
BAM files containing sequencing data from crypts isolated from controls.	Lee-Six et al., 2019	European Genome-phenome Archive (EGA) - accession codes EGA: EGAD00001004192 and EGA: EGAD00001004193
PCAWG mutational signatures.	Alexandrov et al., 2020	https://cancer.sanger.ac.uk/cosmic/signatures
Software and Algorithms
Algorithms and software for calling somatic substitutions - CaVEMan.	Cancer Genome Project, Wellcome Trust Sanger Institute	http://cancerit.github.io/CaVEMan/
Algorithms and software for calling somatic indels - PIndel.	Cancer Genome Project, Wellcome Trust Sanger Institute	http://cancerit.github.io/cgpPindel/
Algorithms and software for calling somatic retrotranspositions - TraFiC-mem.	Rodriguez-Martin et al., 2020	https://gitlab.com/mobilegenomesgroup/TraFiC
Algorithms and software for calling somatic copy number changes - BRASS.	Cancer Genome Project, Wellcome Trust Sanger Institute	https://github.com/cancerit/BRASS
Algorithms and software for calling somatic copy number changes - ASCAT.	Cancer Genome Project, Wellcome Trust Sanger Institute	https://github.com/cancerit/ascatNgs
Algorithms and software for constructing phylogenetic trees - MPBoot.	Hoang et al., 2018	http://www.iqtree.org/mpboot/
Algorithms and software for extracting mutational signatures - HDP.	Roberts, 2018	https://github.com/nicolaroberts/hdp
Algorithms and software for estimating dN/dS ratios.	Martincorena et al., 2017	https://github.com/im3sanger/dndscv
Custom scripts documenting all other analyses.	This paper.	https://github.com/Solafsson/somaticIBD