CRISPR NGS editing check with HISAT2

Before start: Please enable SIMD in your web brower [see Help below].

This tool is for paired end fastq files (for example, xxx_R1_001.fastq.gz and xxx_R2_001.fastq.gz). It uses HISAT2 to find big deletions (treated as introns). Please run the 3 steps below to get the indexed bams from a list of fastq files. In the end, you will get a summary file of called indels and all the bam files to be viewed in IGV.

No spaces are allowed in input file names!

Provide the suffix of your fastq files:

I. Load reference file (a fasta file)

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

III. 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)]:


This tool is a WebAssembly implementation of hisat2. It runs commands like this:

## index the references
hisat2-build-s <your-references.fa> my_index
## make sam files and big indels will be treated as splice
hisat2-align-s -x my_index -1 xxx_R1_001.fastq -2 xxx_R2_001.fastq -S out.sam --pen-noncansplice 0

Although hisat2 can soft clip unmapped fragments, it seems 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:

Enable SIMD for your browser

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

  • chromium based browsers (Google Chrome and Microsoft Edge): seems enabled by default since 2021.;

  • Firefox: go to URL about:config, search javascript.options.wasm_simd, then choose true;

  • Other browers do not seem to support this yet.