BALDR

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. Based on the de novo assembly of RNA-Seq reads, it allows reconstructions using the 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

Using BALDR

Prerequisites:

  1. Trimmomatic 0.32
  2. Trinity v2.3.2 (Newer versions are not compatible)
  3. bowtie2 2.3.0
  4. STAR v2.5.2b
  5. samtools v1.3.1
  6. IgBLAST v1.6.1
  7. seqtk 1.2
  8. Perl 5

Installation: Clone or download the BALDR package using the following prompt on the command line

  • cd BALDR
  • chmod +x BALDR

Command Line Usage:

Single-end reads:    ./BALDR --single <file.fastq.gz> <options>
Paired-end reads:    ./BALDR --paired <R1.fastq.gz,R2.fastq.gz> <options> 

Options:

  --method            One or more reconstruction methods may be specified. For multiple methods, separate arguments only by a 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 for help

Related files

IG_loci
IMGT/human
IgBLAST_DB
Recombinome/human
STAR_genomes