. ├── Example_project_begin │  ├── Foster et al 1999 - Rattus genome annotation.pdf │  ├── Foster et al 1999 - Rattus sequence data - A new pipeline for metagenomics.pdf │  ├── Li et al 2021.pdf │  ├── Manuscript_new1.docx │  ├── Manuscript_new2.docx │  ├── Manuscript_old.docx │  ├── Manuscript_draft.docx │  ├── Manuscript_publish.docx │  ├── Meeting notes Jan 13 2022.docx │  ├── Meeting notes Jan 13 2022 added.docx │  ├── Smith et al 2019.pdf │  ├── data │  │  ├── canis_lupus_genbank.fastq │  │  ├── cow_genbank.fastq │  │  ├── new_data │  │  │  ├── felis_catus.bam │  │  │  ├── felis_catus.fastq │  │  │  ├── rattus_norwegicus.bam │  │  │  └── rattus_norwegicus.fastq │  │  ├── result_analysis1.tsv │  │  └── result_analysis2.tsv │  ├── group-meeting-20211216 final.docx │  ├── group-meeting-20211216 notes.docx │  ├── group-meeting-161221 agenda.docx │  ├── process-sequences.py │  ├── Summary function for linear regression.R │  └── summarize_results.R . ├── Example_project_improved.zip │  ├── README.md │  ├── analyses │  │  ├── result_analysis1.tsv │  │  └── result_analysis2.tsv │  ├── data │  │  ├── genbank_data │  │  │  ├── bos_taurus_genbank.fastq │  │  │  └── canis_lupus_genbank.fastq │  │  └── raw_data │  │  ├── felis_catus.bam │  │  ├── felis_catus.fastq │  │  ├── rattus_norwegicus.bam │  │  └── rattus_norwegicus.fastq │  ├── manuscript │  │  ├── Manuscript_v1.docx │  │  ├── Manuscript_v2.docx │  │  ├── Manuscript_v4.docx │  │  ├── Manuscript_v3.1.docx │  │  └── Manuscript_v3.docx │  ├── meeting_notes │  │  ├── 20220113-group-meeting-v2.docx │  │  ├── 20220113-group-meeting-v1.docx │  │  ├── 20211216-group-meeting-v3.docx │  │  ├── 20211216-group-meeting-v2.docx │  │  └── 20211216-group-meeting-v1.docx │  ├── pdfs │  │  ├── Foster et al 1999 - Rattus genome annotation.pdf │  │  ├── Foster et al 1999 - Rattus sequence data - A new pipeline for metagenomics.pdf │  │  ├── Li et al 2021.pdf │  │  └── Smith et al 2019.pdf │  └── scripts │  ├── process_sequences.py │  ├── Summary function for linear regression.R │  └── summarize_results.R └── tree.txt