This is a simple reference-based mapping and duplicate removal pipeline that works entirely in the browser via Biowasm. Handy for small runs. You can check out source code here.

It performs the following steps:

  1. Trim and merge paired reads with fastp.
  2. Map merged reads to reference with minimap2.
  3. Remove duplicates with samtools markdup.
  4. Report mapping and duplicate removal results with samtools flagstat.
  5. Return unique sequences with samtools.

Upload FASTQ reads:

Upload FASTA reference:

Trimming results:

Mapping and duplicate removal results:
Unique Sequences: