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

    • Shade sequence alignments with nimBoxshade

    This is a duplicate to the app boxshade page. It is just my testing of Nim language. It uses nimBoxshade to create good looking printouts from multiple-aligned protein and DNA sequences.

    Step 1: load alignment file (fasta format)


    add ruler to the alignment?
    add sequence position number?
    create consensus line?
    input is aligned DNA sequences?
    the fraction of sequences that must agree for a consensus (0-1)
    output width

    Foreground color for identical residues
    background color for identical residues
    Foreground color for similar residues
    background color for similar residues

    Example of foreground and background colors:

    seq1 MRDRTHE
    seq2 MKDRLEQ
    seq3 MRDRLPD

    Step 2: Start shading

    Help

    nimBoxshade now only support aligned fasta file as the input file and output a RTF file that can be opened with Word. Please see the github page for more information: https://github.com/pinbo/nimboxshade

    The amino acid similarity matrix is from this paper.