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The biscuitBlaster Pipeline

The biscuitBlaster pipeline combines BISCUIT, samblaster, and samtools to align reads, mark duplicates, sort, and index the aligned reads in an easy one-liner.

Depending on the downstream analysis goals of the user, there are two pipelines available.

Version 1

Version 1 of the biscuitBlaster pipeline is the most basic version, producing a sorted, indexed BAM with duplicate marked reads.

biscuit align -R "my_rg" /path/to/my_reference.fa read1.fq.gz read2.fq.gz | \
    samblaster | samtools sort --write-index -o my_output.bam -O BAM -

where "my_rg" is the read group (if applicable) to be used, /path/to/my_reference.fa is the FASTA file for the reference genome, read*.fq.gz are the read1 and read2 FASTQ files from the sequencing run, and my_output.bam is the name of the output BAM file.

Version 2

Version 2 of the biscuitBlaster pipeline builds off Version 1 by using samblaster generate SAM files of the split and discordant alignments and a FASTQ file of the heavily clipped reads, in addition to generating a duplicate marked, sorted, and indexed BAM file with mate tags added.

biscuit align -R "my_rg" \
    /path/to/my_reference.fa read1.fq.gz read2.fq.gz | \
    samblaster --addMateTags | \
    parallel --tmpdir temp_dir --pipe --tee {} ::: \
        "samblaster -a -e -u clipped.fastq -d disc.sam -s split.sam -o /dev/null" \
        "samtools view -hb | samtools sort -o all_my_reads.bam -O BAM -"
samtools index all_my_reads.bam

Version 2 leverages GNU parallel to produce each of these files in a fast, efficient manner. Note, each of the SAM files produced will likely need to be sorted before using in downstream analyses.

It should also be pointed out that a relatively recent version of GNU parallel is needed to run Version 2 of biscuitBlaster. In our experience, Version 2 has worked with GNU parallel versions >= 20191122.

biscuitBlaster Representations

Version 1 Representation

serial biscuitBlaster

Version 2 Representation

parallel biscuitBlaster