Tools

  • 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

    • Map long reads with minimap2

    Minimap2 + Samtools Mapping Tool

    This tool uses BioWASM to run minimap2 and samtools in your browser.

    fastq files with long reads or short reads can be mapped to a reference by minimap2 and sorted bam files will be created by samtools. You can view the mapping results (bam files) with IGV.

    1. Input Files

    2. Minimap2 Options

    3. Run Analysis

    4. Output

    BioWASM modules loaded and ready.

    Acknowledgement

    This tool was written with the assistance of DeepSeek.