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

    • Filter fastq files with FASTP

    FASTP is a tool designed to provide fast all-in-one preprocessing for FastQ files.
    Please check out the fastp github page for some detailed information:
    https://github.com/OpenGene/fastp

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    No spaces are allowed in input file names!

    Step 1: load fastq files and set filtering options






    Step 2: Start filtering


    Acknowledgement

    1. fastp: https://github.com/OpenGene/fastp
    2. WebAssembly of fastp was compiled from source based on the patch file of https://github.com/biowasm/biowasm/tree/main/tools/fastp with additional option --interleaved_out added.