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Input Formats

hextraza edited this page Mar 20, 2025 · 3 revisions

Overview

nimble supports multiple input formats for sequencing data, allowing flexibility in how reads are provided for alignment. It accepts both single-end and paired-end sequencing reads in FASTQ.GZ and BAM formats.

Supported Input Formats:

  • Single-End Reads:

    • .fastq.gz (compressed FASTQ)
  • Paired-End Reads:

    • Two .fastq.gz files (e.g., reads_R1.fastq.gz and reads_R2.fastq.gz)
  • BAM Files:

    • 10x Genomics BAM files, either paired-end or single-read.

By default, nimble will automatically detect whether the input is single or paired-end based on the provided files. When using BAM input, paired-end reads can be enforced with the --force_bam_paired flag, with all unpaired reads skipped.

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