README 

Dataset: Data from immunocompromised individuals vaccinated with SARS-CoV2 vaccines: antibody titers, B cell receptor repertoire sequencing, and B cell immunophenotyping

Conctact person:
Karin Loré
karin.lore@ki.se

Contents

1. compressed_sequencing_data.tar.gz
   - Compressed archive containing all sequencing data and processed results.
   - Inside this archive:
     - preprocessed_antigen_specific_sanger/: Preprocessed FASTA sequences and QC reports.
     - rawdata/: Original raw sequencing data (Sanger and bulk BCR sequencing).

2. metadata.csv (or .tsv)
   - Contains sample metadata, study group, subgroup based on time, subgroup based on GHVD, and if they had detectable antibody titers.
   - Can be used to map sequencing files to samples and experimental conditions.

Notes
- The compressed archive contains all sequencing data organized into raw and processed subfolders.
- Preprocessed data includes per-sample QC reports generated with SCiFER.
- Rawdata includes original sequencing files before preprocessing.
- File naming conventions:
  - FASTA sequences: per-sample FASTA files in preprocessed_antigen_specific_sanger/
  - Bulk BCR FASTQ files: <sample>-igm_S#_L001_R#.fastq.gz or <sample>-igg_S#_L001_R#.fastq.gz
  - R1/R2 indicates paired-end reads, S# indicates the sample number.
- Refer to the metadata file for mapping sample IDs to sequencing files.
