BLAST

Graph

Usage

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

bash assembly.sh [SAMPLE_ORGANISM_DIR] [REFERENCE_BLAST_DIR]

Multiple samples:

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

bash wrapper_bacteria_blast.sh

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

bash wrapper_virus_blast.sh

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

bash wrapper_fungi_blast.sh

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

bash wrapper_parasite_blast.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.
• 2. Runs BLASTn against reference.
• 3. Runs BLASTx against reference.

Note: This script must be run after assemblying the reads into contigs.

##I/O

• Arguments:

  • $1 (sampleDir) = Directory with the sample analysis. (ANALYSIS/xx-organism/sampleName/)
  • $2 (refDB) = Directory where the blast db is located. (REFERENCES/ORGANISM_GENOME_REFERENCE/BLAST)

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

  • sampleContig: fasta file with the contigs to be used as queries in blast.

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

  • sampleName_blast_log.log: log file for the blast run.
  • sampleName_BLASTn.blast: hit file of the blast.
  • sampleName_BLASTn_filtered.blast: hit file of the blast filtered by % id >90% and query sequence length > 100bp.