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

    • Call variants with exactSNP

    This tool is for calling SNPs and small indels from bam files with subread tool exactSNP. All the operations are within your memory.

    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!

    I. Load the reference (a fasta file)


    II. Load bam files

    III. Call variants

    One vcf file will be created for each bam. A summary tab-delimited text file merging all vcf files will be created too.

    Help

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

    exactSNP -b -i mapping_results.bam -g mm10.fa -o calledSNPs.vcf

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

    Acknowledgement