Table 3.
Summary of the pipeline methodologies (tx: Treatment).
| A | B | C | E | F | J | I | H | |
|---|---|---|---|---|---|---|---|---|
| Storage | −20 °C | −20 °C | NA | −20 °C | −20 °C | −20 °C | −20 °C | −20 °C |
| Enrichment prior extraction | None | None | NA | homogenization, centrifugation, filtration, nuclease tx | Centrifugation, filtration | Homogenization, centrifugation, DNase tx | ||
| DNA extraction | Trizol LS/Phasemaker | Trizol LS/Phasemaker | NA | QIAamp Viral RNA Mini Kit | easyMAG | easyMAG | ||
| RNA extraction | Trizol LS/Phasemaker | Not extracted | NA | Trizol | ||||
| Enrichment after extraction | QuantiTect Whole Transcriptome Kit, Qiagen | None | NA | None | None | None | None | None |
| Library preparation DNA | Nextera XT DNA Library v2 | NA | NEBNext® Ultra™ II DNA Library Prep Kit | Nextera XT | Nextera XT | |||
| Library preparation RNA | NA | TruSeq | ||||||
| Sequencer | MiSeq (2 × 150 bp) | NA | NextSeq (2 × 150 bp) | MiSeq (1 × 150 bp) | HiSeq 2500 & 4000 (2 × 100 bp) | |||
| Reads filtering | adapter trimming (bbduk.sh) | FastQC | Trimmomatic | Trimmomatic | PrinSeq, seqtk trimfq | Trimmo-matic | ||
| Taxonomic classification | k-mer | k-mer + mapping | mapping | mapping | k-mer | mapping | mapping | |
| Tool | bbmap bbsplit | Kraken2 + Bowtie2 | SeqMan NGen software v14 (DNAStar, Lasergene) | bowtie2 | Kraken | bwa mem, blastn | SNAP | |