BALDR 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:
- 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
- IG-mapped_Unmapped (human and rhesus) - Assemble reads mapping to Ig loci + Unmapped reads
- IMGT-mapped (human) - Assemble reads mapping to IMGT V(D)J and C sequences
- Recombinome-mapped (human) - Assemble reads mapping to the Ig recombinome
- FilterNonIG (rhesus)- Assemble reads after filtering those that match to non-Ig genes in the genome
- Trimmomatic 0.32
- Trinity v2.3.2 (Newer versions are not compatible)
- bowtie2 2.3.0
- STAR v2.5.2b
- samtools v1.3.1
- IgBLAST v1.6.1
- seqtk 1.2
- Perl 5
Clone or download the BALDR package.
cd BALDR
chmod +x BALDR
Single-end:
./BALDR --single <file.fastq.gz> <options>
Paired-end:
./BALDR --paired <R1.fastq.gz,R2.fastq.gz> <options>
Options:
--method One or more reconstruction methods. For multiple methods, separte only by comma
human: IG-mapped_Unmapped (default), Unfiltered, IG-mapped_only, IMGT-mapped, Recombinome-mapped
rhesus_monkey: FilterNonIG (default), Unfiltered, IG-mapped_only, IG-mapped_Unmapped
--organism human (default) or rhesus_monkey
--trimmomatic Path for trimmomatic.jar file (e.g. ~/Trimmomatic-0.36/trimmomatic-0.36.jar) (required)
--adapter Path for the Trimmomatic adapter file (e.g. ~/Trimmomatic-0.36/adapters/NexteraPE-PE.fa) (required)
--STAR_index Path for the STAR aligner genome index
--BALDR Path for the BALDR directory (e.g. ~/BALDR) (required)
--memory Max memory for Trinity (default 32G)
--threads number of threads for STAR/bowtie2/Trinity (default 1)
--version Version
--help Print this help
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