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MegaHIT Specifications

Process Details

  • Name: MegaHIT
  • Process UUID: p30om0tg8djpgcqs6vt1u6mvc26t43
  • Process Group: Assembly

Overview

MegaHIT is a short-read assembler designed for metagenomic data assembly. This process takes paired-end FASTQ reads and produces assembled contigs in FASTA format, along with optional statistical analysis of the assembly results. The assembler is particularly well-suited for complex microbial communities and large-scale metagenomic projects.

This process is implemented in Bash, which invokes a Python script for contig statistics calculation when enabled.

Key Functionality

  • Short-Read Assembly: Assembles paired-end FASTQ reads into contigs using the MegaHIT algorithm optimized for metagenomic data
  • Contig Statistics: Optionally calculates comprehensive statistics including contig counts, total assembly size, and mean contig length
  • Quality Control: Generates detailed log files for assembly process monitoring and troubleshooting

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Paired-end sequencing reads for assembly
    • Format: FASTQ files (set)

  • Mate

    • Description: Mate pair information for paired-end reads
    • Format: Mate file

Outputs

  • FASTA File

    • Description: Assembled contigs from the MegaHIT assembly process
    • Format: FASTA (set)

  • Log File

    • Description: Detailed log of the MegaHIT assembly process including runtime information and statistics
    • Format: LOG

  • CSV File

    • Description: Statistical summaries and contig length distributions when statistics option is enabled
    • Format: CSV

  • FASTA

    • Description: Final assembled contigs file
    • Format: FASTA

Parameters & Settings

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

  • Would you like the stats output?

    • Description: Choose 'yes' if you'd like the stats for MegaHIT assembly results.
    • Available options: yes, no (default)

  • MegaHIT Optional Parameters

    • Description: Optional Parameters for MegaHIT Short-Read Assembler
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on calc_ctg_lens.py
  • Related Papers: Li, D., Liu, C. M., Luo, R., Sadakane, K., & Lam, T. W. (2015). MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31(10), 1674-1676.