├── MitoFish_download_links.MD ├── QIIME-compatible ├── 12S-16S-18S-tax.qza ├── 12S-seqs-derep-uniq.qza ├── 12S-tax-derep-uniq.qza └── README.MD ├── README.md ├── db.scripts ├── 12S.unconventional.acc ├── COI.unconventional.acc ├── FotW5_classification │ ├── FotW5Classification.pdf │ ├── FotW5_family.tsv │ ├── FotW5_order.tsv │ └── README.md ├── README.md ├── createpickle.py ├── fasta_dedup.py ├── getpickle.py └── process_qiime2.sh ├── mitohelper.py ├── requirements.txt └── testdata ├── 12S.test.fasta ├── Ecoli.K12MG1655.16S.ref.fasta ├── README.md ├── Zebrafish.12S.ref.fasta ├── Zebrafish.18S.ref.fasta ├── blastnALN.alnpositions.pdf ├── blastnALN.alnpositions.tsv ├── blastnALN.blastn.txt ├── getalignment_out.PNG ├── getrecordOUT_L7.fasta ├── getrecordOUT_L7.taxonomy.tsv ├── getrecordOUT_L7_hits.tsv └── species.query.txt /MitoFish_download_links.MD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/MitoFish_download_links.MD -------------------------------------------------------------------------------- /QIIME-compatible/12S-16S-18S-tax.qza: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/QIIME-compatible/12S-16S-18S-tax.qza -------------------------------------------------------------------------------- /QIIME-compatible/12S-seqs-derep-uniq.qza: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/QIIME-compatible/12S-seqs-derep-uniq.qza -------------------------------------------------------------------------------- /QIIME-compatible/12S-tax-derep-uniq.qza: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/QIIME-compatible/12S-tax-derep-uniq.qza -------------------------------------------------------------------------------- /QIIME-compatible/README.MD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/QIIME-compatible/README.MD -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/README.md -------------------------------------------------------------------------------- /db.scripts/12S.unconventional.acc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/12S.unconventional.acc -------------------------------------------------------------------------------- /db.scripts/COI.unconventional.acc: -------------------------------------------------------------------------------- 1 | JN184086 2 | AB282832 3 | KP266818 4 | -------------------------------------------------------------------------------- /db.scripts/FotW5_classification/FotW5Classification.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/FotW5_classification/FotW5Classification.pdf -------------------------------------------------------------------------------- /db.scripts/FotW5_classification/FotW5_family.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/FotW5_classification/FotW5_family.tsv -------------------------------------------------------------------------------- /db.scripts/FotW5_classification/FotW5_order.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/FotW5_classification/FotW5_order.tsv -------------------------------------------------------------------------------- /db.scripts/FotW5_classification/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/FotW5_classification/README.md -------------------------------------------------------------------------------- /db.scripts/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/README.md -------------------------------------------------------------------------------- /db.scripts/createpickle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/createpickle.py -------------------------------------------------------------------------------- /db.scripts/fasta_dedup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/fasta_dedup.py -------------------------------------------------------------------------------- /db.scripts/getpickle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/getpickle.py -------------------------------------------------------------------------------- /db.scripts/process_qiime2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/db.scripts/process_qiime2.sh -------------------------------------------------------------------------------- /mitohelper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/mitohelper.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/requirements.txt -------------------------------------------------------------------------------- /testdata/12S.test.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/12S.test.fasta -------------------------------------------------------------------------------- /testdata/Ecoli.K12MG1655.16S.ref.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/Ecoli.K12MG1655.16S.ref.fasta -------------------------------------------------------------------------------- /testdata/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/README.md -------------------------------------------------------------------------------- /testdata/Zebrafish.12S.ref.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/Zebrafish.12S.ref.fasta -------------------------------------------------------------------------------- /testdata/Zebrafish.18S.ref.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/Zebrafish.18S.ref.fasta -------------------------------------------------------------------------------- /testdata/blastnALN.alnpositions.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/blastnALN.alnpositions.pdf -------------------------------------------------------------------------------- /testdata/blastnALN.alnpositions.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/blastnALN.alnpositions.tsv -------------------------------------------------------------------------------- /testdata/blastnALN.blastn.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/blastnALN.blastn.txt -------------------------------------------------------------------------------- /testdata/getalignment_out.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/getalignment_out.PNG -------------------------------------------------------------------------------- /testdata/getrecordOUT_L7.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/getrecordOUT_L7.fasta -------------------------------------------------------------------------------- /testdata/getrecordOUT_L7.taxonomy.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/getrecordOUT_L7.taxonomy.tsv -------------------------------------------------------------------------------- /testdata/getrecordOUT_L7_hits.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/getrecordOUT_L7_hits.tsv -------------------------------------------------------------------------------- /testdata/species.query.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aomlomics/mitohelper/HEAD/testdata/species.query.txt --------------------------------------------------------------------------------