├── .gitignore ├── .python-version ├── 01prefetch.sh ├── 02fasterq-dump.sh ├── 03trim_galore_p.sh ├── 03trim_galore_s.sh ├── 04transcriptquant.sh ├── 04trinity_p.cwl ├── 04trinity_p.sh ├── 05AAEA_salmon_p.cwl ├── 05AAEA_salmon_p.sh ├── 05salmon_p.sh ├── 05salmon_s.sh ├── 101Kraken2-build.sh ├── 101Kraken2.md ├── 101Kraken2.sh ├── 102Kraken2-run.sh ├── 11TransDecoder.sh ├── 12GetRefProts.sh ├── 13makeBLASTdb.sh ├── 13runBLASTp.sh ├── 15ggsearch.sh ├── 15mkannotbl.pl ├── 15parseggsearch.pl ├── 15parseggsearch.sh ├── 16HMMscan.sh ├── 16mkannotbl_pfam.pl ├── 16tbl2oneline.pl ├── LICENSE ├── README.md ├── SRR.txt ├── create_ref16s.py ├── kraken2_report_formatter.py └── kraken2headder ├── __init__.py ├── add_taxonomy.py └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bonohu/SAQE/HEAD/.gitignore -------------------------------------------------------------------------------- /.python-version: 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