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

    • Short read de novo assembly with Velevet

    Velvet is software to perform dna De novo assembly from short reads by manipulating de Bruijn graphs. Some introduction can be found here: Introduction to de novo assembly with Velvet. It is an old software and recently SPAdes is the most popular de novo assembler. I used Velvet here simply because it is easy to be exported to WebAssembly and it is good enough for simple projects like gene/plasmid assembly.

    You can read the Velvet manual or the SPAdes instructions for some parameter setting suggestion.

    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!

    Step 1: load fastq files and set assembling parameters








    Step 2: Start Assembling

    Acknowledgements

    1. velvet: https://github.com/dzerbino/velvet
    2. biowasm project for easy exporting C/C++ tools to WebAssembly.