A read group (@RG) is a unique identifier that group reads together, capturing relevant information about the sample and the sequencing process and technology, utilized by various downstream bioinformatics tools.
The relevant fields in defining a read group include:
- ID (Identifier): A unique identifier for the read group within the BAM file and across multiple BAM files used in the same dataset.
- SM (Sample): The sample to which the reads belong.
- PL (Platform): The technology used to sequence the reads (e.g., ONT).
- PM (Platform Model): The platform model reflecting the instrument series.
- PU (Platform Unit): A unique identifier for the sequencer unit used for sequencing.
- LB (Library): The library used to sequence the reads.
- DS (Description): Semantic information about the reads in the group, encoded as a semicolon-delimited list of “Key=Value” strings.
- DT (Date/Time): The date and time when the run was produced (ISO8601 date or date/time).
- basecall_model: The model used for base calling.
The original read groups from the unaligned BAM files are linked and maintained in the corresponding alignment BAM files. In-house bash code that utilizes samtools replaces SM and LB information with the correct identifiers used by the portal, as follows:
- SM:
<sample name> - LB:
<sample name>.<library>
E.g., in BAM file:
@RG ID:bcdb4058-3545-4c45-aea9-4159f1c2ca7d_dna_r10.4.1_e8.2_400bps_sup@v4.2.0 DT:2024-02-21T12:56:53.022625-06:00 DS:runid=bcdb4058-3545-4c45-aea9-4159f1c2ca7d basecall_model=dna_r10.4.1_e8.2_400bps_sup@v4.2.0 LB:SMACUWVOKOZU.SMALI56YAYM5 PL:ONT PM:3A PU:PAW14872 al:unclassified SM:SMACUWVOKOZU
All the relevant code is accessible in the GitHub repository:
- ImportReadGroups_methylink.sh [ImportReadGroups]