Tools

  • Plasmid Viewer
  • KASP cluster
  • Barley Imputed spike smFISH
  • Imputed JD99 Wheat spike smFISH
  • JD99 Wheat spike smFISH
  • Plant pegRNA designer
  • Multiple sequence alignments
  • 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

    • Demultiplex long reads FASTQ files

    This tool can be used to demultiplex a fastq file (long reads or merged paired-end reads with barcodes on both ends). It supports both gzipped and uncompressed fastq files. The tool allows users to specify the left and right adapter sequences, as well as the lengths of the barcodes. It also provides options for trimming the adapter sequences from the reads.

    Two modes are supported. Your reads should have one of the following structures:

    Both ends: [LeftBarcode][LeftAdapter]...[RightAdapter][RightBarcode]

    5' end only (single adapter + barcode): [Barcode][Adapter]...

    Step 1: Upload FASTQ File

    Supports .fastq, .fq (uncompressed or gzipped)

    Step 2: Configure Barcodes

    Barcode layout:

    Enter your barcode sequences and sample names:

    Sample Name Index 1 Sequence Index 2 Sequence Action

    Upload a tab-delimited file with barcode information (sample name, index 1, index 2):

    Format: SampleName<tab>Index1<tab>Index2 (one per line)

    Preview (only show top 5 rows):

    Sample Name Index 1 Sequence Index 2 Sequence

    Adapter Sequences
    Detection Method:

    1. Find left adapter in first 30bp → extract left barcode before it

    2. Find reverse complement of right adapter in last 30bp → extract right barcode after it

    3. If not found, swap adapters and repeat search

    Detection Method:

    1. Find adapter in the first N bp (search window) → extract barcode before it

    2. If not found and reverse strand is enabled, find reverse complement of the adapter in the last N bp → extract reverse complement of the barcode after it

    Barcode Settings


    Step 3: Run Demultiplexing

    Demultiplexing Results

    Acknowledgement

    This tool was written with the assistance of DeepSeek.