Scripts developed for Orange and San Luis Obispo County Public Health Laboratories
To Start: GISAID_Uploads/Start.sh
- Create a new RUN directory with naming convention "SLO_2021-10-05"
- Data source (PHL) _ yyyy-mm-dd
- Enter new RUN directory
- Add metadata to RUN directory
- Create a "BaselineSamples.csv" file with Sample ID and baseline surveillance
- Create new directory "Fasta_Pieces"
- Fill Fasta_Pieces with individual assemblies
- Run GISAID_Uploads/Start.sh according to GISAID_Uploads/README.md
What This Does:
- Format Assemblies for GISAID
- Take individual assemblies, change headers to "hCoV-19/USA/CA-{name here}-##/2021"
- Concatenate files into All_good.fasta
- Format Assemblies for Aspen
- Just concatenate files
- Format Assemblies for GenBank
- Takes input of Baseline surveillance status
- Adds keyword to fasta header of surveillance samples
- Perform Assembly_QC on Samples
- Checks coverage
- Checks # of consecutive unambiguous nucleotides (>10k)