The biscuitSifter Pipeline

The biscuitSifter pipeline combines BISCUIT, dupsifter, and samtools to align reads, mark duplicates, sort, and index the aligned reads in an easy two-step process.

biscuit align \
    -@ NTHREADS \
    /path/to/my_reference.fa \
    read1.fq.gz \
    read2.fq.gz | \
dupsifter /path/to/my_reference.fa | \
samtools sort -@ NTHREADS -o my_output.bam -O BAM -

samtools index my_output.bam

where NTHREADS is the number of threads, /path/to/my_reference.fa is the FASTA file for the reference genome, read*.fq.gz are the FASTQ files for reads 1 and 2 from the sequencing run, and my_output.bam is the name of the output BAM file.

The --write-index option in samtools sort can alternatively be used to simplify the two-step process into a single command:

biscuit align \
    -@ NTHREADS \
    /path/to/my_reference.fa \
    read1.fq.gz \
    read2.fq.gz | \
dupsifter /path/to/my_reference.fa | \
samtools sort \
    -@ NTHREADS \
    --write-index \
    -o my_output.bam \
    -O BAM \
    -