KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains (parasite strains) | ||
| Cryptosporidium hominis (12146 isolates) | This paper | N/A |
| Cryptosporidium hominis (103 isolates) | SRA | https://www.ncbi.nlm.nih.gov/sra/ |
| Critical commercial assays | ||
| FastDNA SPIN Kit for Soil | MP Biomedicals | Cat#116560–200 |
| Q5 Hot Start High-Fidelity 2X master mix | New England Biosciences | Cat#M0494S |
| Dynabeads Anti-Cryptosporidium kit | Invitrogen | Cat#73011 |
| Qiagen DNeasy Blood & Tissue Kit | QIAGEN | Cat#69504 |
| QIAamp DNA Mini kit | QIAGEN | Cat#51304 |
| REPLI-g Midi Kit | QIAGEN | Cat#150043 |
| Oligonucleotides | ||
| Primer: C. hominis 18S rRNA | Xiao et al.32 | N/A |
| Primer: C. hominis gp60 | Alves et al.33 | N/A |
| Software and algorithms | ||
| CLC Genomics Workbench | QIAGEN | https://digitalinsights.qiagen.com |
| SPAdes v3.1 | St. Petersburg State University | http://cab.spbu.ru/software/spades/ |
| Blastn v2.10.1 | NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| MUSCLE v3.8.31 | EMBL-EBI | https://www.ebi.ac.uk/ |
| RAxML-NG v1.0.0 | Kozlov et al.34 | https://github.com/amkozlov/raxml-ng |
| jModelTest v2.1.10 | Posada35 | https://github.com/ddarriba/jmodeltest2/releases |
| BWA-MEM v0.7.17 | Li and Durbin36 | https://github.com/lh3/bwa |
| SAMtools v1.7 | SAMtools | http://samtools.sourceforge.net/ |
| BCFtools v1.12 | SAMtools | https://samtools.github.io/bcftools/ |
| GATK4 | Broad Institute | https://gatk.broadinstitute.org/hc/en-us |
| SnpEff | Pablo Cingolani | https://pcingola.github.io/SnpEff/ |
| Vcftools 0.1.16 | Vcftools | https://vcftools.github.io/index.html |
| PLINK v1.90 | PLINK | http://zzz.bwh.harvard.edu/plink/ |
| LDAK v5.1 | Speed et al.37 | https://dougspeed.com/ldak/ |
| ggplot2 | R | https://www.rdocumentation.org/packages/ggplot2/versions/3.3.5 |
| Structure v.2.3.4 | Stanford University | https://web.stanford.edu/group/pritchardlab/structure.html |
| Pophelper v2.3.1 | R | http://www.royfrancis.com/pophelper/articles/index.html |
| DnaSP v6.12.03 | Rozas et al.38 | http://www.ub.edu/dnasp/ |
| POPart v1.7 | Allan Wilson Centre | http://popart.otago.ac.nz |
| hmmIBD v2.0.4 | Schaffner et al.39 | https://github.com/glipsnort/hmmIBD |
| Cytoscape v3.9.1 | National Institute of General mMedical Sciences | https://cytoscape.org/ |
| SplitsTree5 | Huson and Bryant40 | https://github.com/husonlab/splitstree5 |
| Phyml v3.3 | Guindon et al.41 | http://www.atgc-montpellier.fr/phyml/ |
| Twist.py | Github | https://github.com/simonhmartin/twisst |
| PlotTwist | Github | https://github.com/JoachimGoedhart/PlotTwist |
| TreeMix v1.13 | Institut Pasteur | https://bitbucket.org/nygcresearch/treemix/ |
| Genomics_general | Github | https://github.com/simonhmartin/genomics_general |
| Other | ||
| Sequence data (146 isolates) | This paper | BioProject:PRJNA821705 |
| Information on samples | This paper | Table S1 and Mendeley Data: https://doi.org/10.17632/g6tr57tb2c.1 |