BALDR is a pipeline tool to build immunoglobulin(Ig)/B cell receptor(BCR) sequences from Illumina single-cell RNA-Seq data. The BALDR offers the following reconstruction methods for human and rhesus macaque: 1. Transcript assembly using all reads with a selected Ig model, 2. Read assembly mapped to Ig loci, and alternatively including unmapped reads. For human sequences only: 1. Read assembly mapping to IMGT V(D)J and C sequences, 2. Reas assembly mapping to the Ig recombinome. For rhesus macaque, it can assemble reads filtered not to match Ig genes. The BALDR pipeline requires the following tools: Trimmomatic 0.32, Trinity v2.3.2, bowtie2 2.3.0, STAR v2.5.2b, samtools v1.3.1, IgBLAST v1.6.1, seqtk 1.2, and Perl 5.
Immunoproteins, genes and antigens; RNA-seq
Upadhyay AA, Kauffman RC, Wolabaugh AN, Cho A, Patel NB, Reiss SM, Havenar-Daughton C, Dawoud RA, Tharp GK, Sanz I, Pulendran B, Crotty S, Lee FE, Wrammert J, Bosinger SE "BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data." Genome Med. 2018 Mar 20;10(1):20. https://doi.org/10.1186/s13073-018-0528-3
PMID: 29558968
PMCID: PMC5859752
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