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# Synergistic effect of short- and long-read sequencing on functional meta-omics
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# About
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## About
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Synergistic effect of short- and long-read sequencing on functional meta-omics:
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Method testing and analyses of Oxford Nanopore Technology (ONT) sequencing runs.
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## Important info
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- [Manuscript](https://docs.google.com/document/d/1TmenUZGwTGU4wIljxwxprZ5L75So8hYSYL5QMzSH9_M/edit?usp=sharing)
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*NOTE: For further notes, e.g. preprocessing of raw reads, create a new page and add a link here*
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- assembly approaches: LR, SR and hybrid
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- assembly comparison w.r.t.
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- basic stat.s (length, contiguity, coverage)
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- seq. similarity (incl. unique seq.s)
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- genomic reconstruction (plasmids, CRISPR, rRNA genes, AMR genes)
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- gene content (common/unique genes)
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- GDB sample:
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- metaG and metaT coverage (contigs and genes)
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- functional characterization and peptide identification (w/ metaP)
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## Datasets
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Datsets analyzed in this study
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- Zymo mock community
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- XXX
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- XXX
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- [Dataset GDB](Dataset-GDB)
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- [The origins of the study](ONT_pilot_w_GDB_samples)
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- Human fecal sample: metaG (Illuminar, ONT), metaT (Illumina), metaP
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- Data obtained by sequencing "generous donor B" across several runs
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- [The origins of the study](ONT_pilot_w_GDB_samples)
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- Original data prepared by Rashi (post-sequencing)
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- Initial analyses performed by CCL
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## Goal
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SR vs. LR vs. hybrid approaches compared w.r.t.
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- Genomic reconstruction
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- Plasmids
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- CRIPR arrays
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- Functional characterization
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- Peptide identification (w/ metaP)
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## Analysis
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[How to run the pipeline](Pipeline)
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- Preprocessing
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- SR
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- QC
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- LR
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- Base calling
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- QC
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- Assembly
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- SR
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- LR
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- Polishing
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- Hybrid
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- Annotation
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- Gene calling
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- Plasmid prediction
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- CRISPR arrays
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- [AMR genes](AMR-genes-prediction)
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- Analysis
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- Figures,tables
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- Report
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## Files
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- Manuscript
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- [v1](https://docs.google.com/document/d/1TmenUZGwTGU4wIljxwxprZ5L75So8hYSYL5QMzSH9_M/edit?usp=sharing)
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- Data
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- Raw data backup: `/work/projects/ecosystem_biology/ONT/`
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- GDB (2019): `GDB.2019.rawdata.*` |
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\ No newline at end of file |
