home.md

+# Synergistic effect of short- and long-read sequencing on functional meta-omics
+
+## Important info
+
+- [Manuscript](https://docs.google.com/document/d/1TmenUZGwTGU4wIljxwxprZ5L75So8hYSYL5QMzSH9_M/edit?usp=sharing)
+
+*NOTE: For further notes, e.g. preprocessing of raw reads, create new pages and add a link here*
+
+## Data
+
+- Metagenomic sequencing
+  - Fecal sample from "generous donor B"
+  - Short reads (Illumina) (SR)
+  - Long reads (ONT) (LR)
+- Meta-omics
+  - metagenomics (metaG)
+  - metatrscriptomics (metaT)
+  - metaproteomics (metaP)
+
+## Goal
+
+SR vs. LR vs. hybri compared w.r.t.
+- Genomic reconstruction
+  - Plasmids
+  - CRIPR arrays
+- Functional characterization
+- Peptide identification (w/ metaP)
+
+## Analysis
+
+- Preprocessing
+  - SR
+    - QC
+  - LR
+    - Base calling
+    - QC
+- Assembly
+  - SR
+  - LR
+    - Polishing
+  - Hybrid
+- Annotation
+  - Gene calling
+  - Plasmid prediction
+  - CRISPR arrays
+  - AMR genes
+- Analysis
+- Figures,tables
+- Report
+