Sequence Interleaver

Interleave paired-end reads from R1 and R2 files for NGS data processing and analysis.

Interleaving Preview (First 2 Pairs)

What is Sequence Interleaver?

This tool interleaves paired-end sequencing reads from separate R1 (forward) and R2 (reverse) files into a single file. Essential for NGS pipelines that require interleaved input format.

How to Use This Tool

  1. Paste or upload R1 reads (forward)
  2. Paste or upload R2 reads (reverse)
  3. Choose format (FASTQ or FASTA)
  4. Select interleaving pattern
  5. Download interleaved file

When to Use

  • Preparing paired-end data for assembly
  • Converting split files to interleaved format
  • Merging Illumina R1/R2 files
  • Input for tools requiring interleaved reads

Interleaving Patterns

Alternating: R1[1], R2[1], R1[2], R2[2]...

Paired blocks: R1[1]+R2[1], R1[2]+R2[2]...

Most tools expect alternating format.

File Format Support

FASTQ: 4-line format with quality scores

FASTA: 2-line format, sequences only

Maintains original read identifiers with /1 and /2 suffixes.

FAQ

Q: What if read counts don't match?
A: The tool will warn you and process only matched pairs.

Q: Are read IDs modified?
A: IDs get /1 and /2 suffixes to indicate pair position.