Tools

  • Gene ID conversion between Kronos and CS
  • Find wheat potential homeologs
  • Extract cDNA sequences
  • Short read de novo assembly with Velevet
  • CRISPR editing check with BWA and SAMTOOLS v2
  • CRISPR NGS editing check with HISAT2
  • Make bam files with strobeAlign
  • Shade sequence alignments with nimBoxshade
  • Shade sequence alignments with Boxshade
  • Design KASP primers with Primer3 v2.5.0
  • Convert a vcf file to SNP table
  • Call variants with exactSNP
  • Index bams with SAMTOOLS
  • Format FASTA to fixed length
  • Make bams and indel calls with Subread
  • Filter fastq files with FASTP
  • Filter multiple fastq files with FASTP
  • Make bam files with BWA and SAMTOOLS
  • CRISPR Editing Analysis v2
  • Demultiplex a Fastq File
  • CRISPR Editing Analysis
  • Call SNPs from multiple sequence alignment
  • Reverse complement of DNA sequences

    • Make bam files with strobeAlign

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

    This tool can take paired end fastq files (for example, xxx_R1_001.fastq.gz and xxx_R2_001.fastq.gz) or single end or merged fastq files. Please run the 3 steps below to get the indexed bams from a list of fastq files.

    Recommend using private browser windows to avoid troubles caused by cookies and caches (open from the menu at the topright corner)

    No spaces are allowed in input file names!

    Provide the suffix of your fastq files if paired end reads:


    I. Choose reference file (a fasta file)

    II. Choose demultiplexed fastq(.gz) files

    III. Map reads and create bam files

    After loading the template fasta file and all the fastq files, now we will use strobeAlign and samtools to create indexed bam files for viewing in the software IGV.

    Alignment parameters (change unless you know what you are doing):
    matching score
    mismatch penalty
    gap open penalty
    gap extension penalty
    bases to be trimmed off from each end of the read when calling variants
    Addition parameters for strobeAlign     

    Help

    This tool is a WebAssembly implementation of strobeAlign, SAMTOOLS and subread exactSNP. It runs commands like this:

    ## map reads to the templates with strobealign
strobealign <your-references.fa> <R1.fastq.gz> <R2.fastq.gz> > out.sam
## make sorted bam files with samtools
samtools sort out.sam > out.bam
samtools index out.bam
## call variants with subread exactSNP (exactSNP has a bug calling sorted bams, so use sams here)
exactSNP -i out.sam -g your-reference.fa -o calledSNPs.vcf

    strobeAlign can detect SNPs and relative large indels from CRIPSR editing. For better SNP and small indels (<10bp), bwa mem seems more accurate. For structure variations like inversions, please try subread or my web app Make bams and indel calls with Subread.

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

    Enable SIMD for your browser

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

    • chromium based browsers (Google Chrome and new Microsoft Edge): go to URL chrome://flags/, search WebAssembly SIMD support, and select “Enabled”; 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.

    Acknowledgement

    Thank Robert Aboukhalil for his development of aioli and biowasm. I successfully compiled strobeAlign, samtools and Subread by learning the patch and compiling scripts from biowasm.