The study to seek the early stage CRC-associated community. The software versions used in this study are written below.
| Tools | Versions | Options | Links | Others |
|---|---|---|---|---|
| MetaPhlAn 4 | 4.1.1 | --index mpa_vJun23_CHOCOPhlAnSGB_202307 -t rel_ab_w_read_stats –add_viruses | https://github.com/biobakery/MetaPhlAn | for Taxonomic Profiling |
| Fastspar | 1.0.0 | --identify-adapters | fastspar_bootstrap --number 1000, fastspar --iterations 50, fastspar_pvalues --permutations 1000 | Correlation Analysis |
| Flye | 2.9.2-b1786 | --pacbio-hifi | https://github.com/mikolmogorov/Flye | |
| Prokka | 1.14.6 | https://github.com/tseemann/prokka | ||
| Pseudofinder | 1.14.6 | https://github.com/filip-husnik/pseudofinder | ||
| DIAMOND | 0.9.10.111 | https://github.com/bbuchfink/diamond | ||
| FastANI | 1.33 | https://github.com/ParBLiSS/FastANI | ||
| BLAST+ | 2.14.0 | blastn -outfmt 6 -perc_identity 85 | reference is publicly distributed from DDBJ[https://www.ddbj.nig.ac.jp/ddbj-releases-e.html], April 2023, including 1,399,781 sequences Last published date in the present data: February 2023 | |
| CheckM | 1.2.0 | https://github.com/Ecogenomics/CheckM | ||
| HMMER | 3.1b2 | http://hmmer.org/ | reference is publicly distributed from EMBL-EBI[ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz], Downloaded on 17 Oct 2025 | |
| panaroo | 1.5.2 | --clean-mode strict --remove-invalid-genes | https://github.com/gtonkinhill/panaroo | Pangenome analysis |
| gapseq | 1.2 c80d1a8e | https://gapseq.readthedocs.io/en/latest/ |
| Tools | Versions | Commands Options | Others |
|---|---|---|---|
| SciPy | 1.7.3 | ||
| lifelines | 0.30.0 | https://github.com/CamDavidsonPilon/lifelines |