Provide the suffix of your fastq files:


I. Load reference file (a fasta file)

  1. Load demultiplexed fastq(.gz) files (adapters need to be trimmed)

  1. Map reads and create bam files

After loading the template fasta file and all the fastq files, now we will use hisat2 to map reads to your templates and use exactSNP to call variations.

Addition parameters for HISAT2     
Addition parameters for exactSNP

Running Summary [you can also check the debug information with the brower developer tool (Ctrl+Shift+I for Chrome and Firefox)]:


Help

This tool is a WebAssembly implementation of hisat2.

Although hisat2 can soft clip unmapped fragments, it can map more reads when using adapter-trimmed reads. So please trim adapters when demulitiplexing your fastq files and when filtering the fastq files with fastp.

Visit the GitHub page for more details: https://github.com/pinbo/bwa-samtools-web.

Enable SIMD for your browser

hisat2 needs SIMD for vector calculation. Please enable it in your web brower first (just need to do once).