BALDR (BCR Assignment of Lineage by De novo Reconstruction) is a pipeline for reconstructing human or rhesus macaque immunoglobulin(Ig)/B cell receptor(BCR) sequences from single cell RNA-Seq data generated by Illumina sequencing.

BALDR is based on the de novo assembly of RNA-Seq reads. It allows reconstructions using following methods:

• IG-mapped_Unmapped (human and rhesus) - Assemble reads mapping to Ig loci + Unmapped reads [default for human]
• FilterNonIG (rhesus)- Assemble reads after filtering those that match to non-Ig genes in the genome [default for rhesus]
• Unfiltered (human and rhesus) - Use all reads for assembling transcripts and select Ig transcript models
• IG-mapped_only (human and rhesus) - Assemble reads mapping to Ig loci
• Recombinome-mapped (human) - Assemble reads mapping to the Ig recombinome
• IMGT-mapped (human) - Assemble reads mapping to IMGT V(D)J and C sequences

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