Blast - AndreaRP/METAGENOMICS GitHub Wiki
Single sample: [blast.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/blast.sh)
bash assembly.sh [SAMPLE_ORGANISM_DIR] [REFERENCE_BLAST_DIR]
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.
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- Creates necessary directories.
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- Runs BLASTn against reference.
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- Runs BLASTx against reference.
Note: This script must be run after assemblying the reads into contigs.
##I/O
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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)
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Input Files: (In ANALYSIS/xx-organism/sampleName/contigs/)
- sampleContig: fasta file with the contigs to be used as queries in blast.
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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.