Assembly - AndreaRP/METAGENOMICS GitHub Wiki

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Usage

Single sample: [assembly.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/assembly.sh)

bash assembly.sh [MAPPED_READ_DIR]

Multiple samples:
Bacteria: [wrapper_bacteria_assembly.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_bacteria_assembly.sh)

bash wrapper_bacteria_assembly.sh

Virus: [wrapper_virus_assembly.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_virus_assembly.sh)

bash wrapper_virus_assembly.sh

Fungi: [wrapper_fungi_assembly.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_fungi_assembly.sh)

bash wrapper_fungi_assembly.sh

Parasite: [wrapper_parasite_assembly.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_parasite_assembly.sh)

bash wrapper_parasite_assembly.sh

Note: To run any of wrapper scripts above you must have generated the sample name list with Sample Name list generator

In a nutshell...

    1. Creates necessary directories.
    1. Assembles fastq files with spades.
    1. Runs quast to check alignment quality

Note: This script should be run after mapping with a reference.

##I/O

  • Arguments:

    • $1 (mappedDir) = Group Directory. Directory where the fastq to be assembled are located. (ANALYSIS/xx-organism/sampleName/reads)

  • Input Files: (In ANALYSIS/xx-organism/sampleName/reads)

    • mappedR1Fastq = R1 alignment file.
    • mappedR2Fastq = R2 alignment file.

  • Output files: (In ANALYSIS/xx-organism/sampleName/contigs)