Tools

  • Plant pegRNA designer
  • Multiple sequence alignment with Kalign
  • Demultiplex long reads FASTQ files
  • Map long reads with minimap2
  • Concatenate files
  • 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

    • Plant pegRNA designer

    PlantPegDesigner

    The plant pegRNA design website (www.plantgenomeediting.net/) does not function recently, so I converted the perl script underneath it to a javascript-based html tool with the help of Claude AI.


    Citation: pegRNAs used in this study were designed with the webtool (https://junli.netlify.app/apps/plant-pegrna-designer/), which was rewritten with javascript based on the source code of PlantPegDesigner (Lin et al. 2021).


    Lin, Q., Jin, S., Zong, Y. et al. High-efficiency prime editing with optimized, paired pegRNAs in plants. Nat Biotechnol 39, 923–927 (2021). https://doi.org/10.1038/s41587-021-00868-w

    Input Parameters

    Allele change is marked as "(a/b)". "a" is the original sequence and "b" is the designed mutation sequence. "a" or "b" could be null value to represent the deletion "(a/)" or insertion "(/b)"