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

    • Make bams and indel calls with Subread

    This tool is for paired end fastq files (for example, xxx_R1_001.fastq.gz and xxx_R2_001.fastq.gz).
    Please run the 3 steps below to get the indexed bams from a list of fastq files.
    Please make sure you have at least 1.5 Gb of free memory.

    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!

    Provide the suffix of your fastq files:


    I. Load reference file (a fasta file)

    Requirement: each line should be <1000 bp, othewise please format your fasta here.

    II. Load demultiplexed fastq(.gz) files

    III. Map reads and create bam files

    After loading the template fasta file and all the fastq files, now we will use subread to create indexed bam files for viewing in the software IGV and call indels and structure variations.

    Running Summary [you can also check the debug information with the brower developer tool (Ctrl+Shift+I for Chrome and Firefox)]:

    Help

    This tool is a WebAssembly implementation of subread. It runs commands like this:

    ## index the references
subread-buildindex -M 1000 -o my_index <your-references.fa>
## make sorted bam files and vcf files for indels (<=16 bp) 
#  and structure variaitons (indels > 16 bp and inversions etc)
subread-align -i my_index -r xxxx_R1_001.fastq.gz -R xxxx_R2_001.fastq.gz
              -o xxxx.bam -I 16  -sv --sortReadsByCoordinates

    Now it can detect any size of deletions but only < 17 bp of insertions.

    Visit the GitHub page for more details: https://github.com/pinbo/bwa-samtools-web.

    Notes

    • If this web app did not work for you, you can also try the R script that uses Rsubread.
    • If IGV cannot load your bams (or shows nothing), it is possible due to bad index. You can remake the bam indexes with the tool Index bams with SAMTOOLS. Then replace the old indexes.

    Acknowledgement