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Run Alignments Specifications

Process Details

  • Name: run_alignments
  • Process UUID: f931lrv2i9ku9q2do7uizt075sab04
  • Process Group: Annotation

Overview

This process aligns concatenated fastq files against a filtered ORF database using Diamond BLASTX for protein sequence alignment. The process performs high-throughput sequence alignment to identify protein-coding sequences and quantify their abundance in the sequencing data.

This process is implemented in Bash, which invokes Diamond BLASTX for protein sequence alignment.

Key Functionality

  • Protein Sequence Alignment: Performs BLASTX alignment of nucleotide sequences against a protein reference database using Diamond
  • Memory-Optimized Processing: Uses configurable block sizes to manage memory consumption during alignment
  • Abundance Quantification: Processes alignment results to generate counts of unique sequence matches
  • Parallel Processing: Utilizes multiple CPU threads for efficient alignment processing

Input/Output Specification

Inputs

Required Inputs

  • DiamondDatabase

    • Description: Pre-built Diamond database containing filtered ORF sequences for alignment
    • Format: dmnd

  • reads

    • Description: Set of concatenated fastq files containing sequencing reads to be aligned
    • Format: fastq

Outputs

  • outFileTSV

    • Description: Tab-separated file containing alignment results with sequence counts and unique match quantification
    • Format: tsv

  • logOut

    • Description: Log file containing Diamond alignment process information and statistics
    • Format: out

Parameters & Settings

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

  • Diamond Block Size
    • Description: The block size, measured in billions of sequence letters to be processed, affects memory consumption; higher block sizes lead to higher memory usage.
    • Default value: 6

References & Resources

  • Tool Documentation: Contact the team for details on Diamond BLASTX alignment parameters
  • Related Papers: Buchfink, B., Xie, C. & Huson, D.H. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015). https://doi.org/10.1038/nmeth.3176