# earlyStageCRC
The study to seek the early-stage specific CRC signatures.
The software versions used in this study are written below.
| Tools | Versions | Options | Links | Others |
|---|---|---|---|---|
| BLAST+ | 2.2.30 | 16SrRNA gene detection with VITCOMIC2 | ||
| mOTUs | 3.0.3 | max_tax, calc_mgc, calc_motu | https://github.com/motu-tool/mOTUs | ref_mOTU_3.0.3 meta_mOTU_3.0.3, for Taxonomic Profiling |
| 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 |
| AdapterRemoval | 2.3.3 | --identify-adapters | ||
| bowtie2 | 2.2.9 | --no-hd --no-sq --fast-local | Phix removal from shotgun metagenomic reads | |
| seqkit | 2.2.0 | seq -m 50 | length filtering | |
| MEGAHIT | 1.2.9 | –min-contig-len 1500 parameter | ||
| Flye | 2.9.2-b1786 | --pacbio-hifi | https://github.com/mikolmogorov/Flye | |
| Prokka | 1.14.6 | https://github.com/tseemann/prokka | ||
| FastANI | 1.33 | https://github.com/ParBLiSS/FastANI | ||
| CheckM | 1.2.0 | https://github.com/Ecogenomics/CheckM | ||
| GTDB-Tk | 2.1.1 | classify_wf -x fa | release 207_v2 | |
| dRep | 2.3.2 | dereplicate --S_ani 0.99 -comp 99 -con 1 | https://github.com/MrOlm/drep | |
| 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 | |
| barrnap | 0.9 | https://github.com/tseemann/barrnap | ||
| MetaPhlAn 4 | 4.1.1 | marker gene extraction ,mpa_vJun23_CHOCOPhlAnSGB_202403 | ||
| Prokka | 1.14.6 | --compliant --rfam | https://github.com/tseemann/prokka | Preparetion of pseudogene detection |
| Unicycler | 0.5.1 | https://github.com/rrwick/Unicycler | ||
| Pseudofinder | 1.14.6 | https://github.com/filip-husnik/pseudofinder | ||
| DIAMOND | 0.9.10.111 | https://github.com/bbuchfink/diamond | ||
| Panaroo | 1.5.2 | |||
| samtools | 1.19.2 |
| Tools | Versions | Commands Options | Others |
|---|---|---|---|
| SciPy | 1.7.3 | ||
| matplotlib-venn | v 0.11.9 | ||
| clustal omega in Biopython | v 1.79 |