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Map Reads Specifications

Process Details

  • Name: map_reads
  • Process UUID: f93190600044z80ama3x770emf99sl
  • Process Group: Laava

Overview

This process aligns sequencing reads to reference sequences for AAV (Adeno-Associated Virus) analysis. The process maps reads against vector, packaging, and host reference sequences to enable downstream analysis of viral vector characteristics and contamination assessment.

This process is implemented in Bash, which invokes a shell script for read alignment using Minimap2.

Key Functionality

  • Read Alignment: Maps sequencing reads to multiple reference sequences including AAV vector, packaging plasmid, and host genome
  • Multi-Reference Mapping: Supports alignment against vector, packaging, and host reference sequences simultaneously
  • Paired-End Support: Handles both single-end and paired-end sequencing data
  • Compressed File Handling: Automatically processes gzipped input files

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Sequencing reads to be aligned (single-end or paired-end)
    • Format: FASTQ

  • Vector FASTA

    • Description: AAV vector reference sequence
    • Format: FASTA

  • Mate

    • Description: Sequencing configuration specifying single-end or paired-end reads
    • Format: mate

Optional Inputs

  • Packaging FASTA

    • Description: Packaging plasmid reference sequence for contamination detection
    • Format: FASTA

  • Host FASTA

    • Description: Host genome reference sequence for contamination assessment
    • Format: FASTA

Outputs

  • BAM File

    • Description: Aligned reads in binary alignment format
    • Format: BAM

  • BAM Index

    • Description: Index file for the BAM alignment file enabling rapid access
    • Format: BAM_BAI

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

Parameters for this process are configured through the container environment and are not directly user-configurable through the UI.

References & Resources

  • Tool Documentation: Contact the team for details on map_reads.sh
  • Related Papers: Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100. doi:10.1093/bioinformatics/bty191