Created
June 12, 2020 19:30
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docker blastn
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| docker run -it -v $PWD:$PWD --name blast_nt ncbi/blast | |
| update_blastdb.pl --showall [*] | |
| #cd /media/jochum00/Aagaard_Raid/reference_datasets/ncbi_db | |
| #mkdir nt | |
| #cd nt | |
| update_blastdb.pl --decompress --source gcp --verbose --verbose nt | |
| export BLASTDB=/media/jochum00/Aagaard_Raid/reference_datasets/ncbi_db/nt | |
| blastn \ | |
| -task megablast \ | |
| -max_target_seqs 1 \ | |
| -num_threads 32 \ | |
| -db_soft_mask 30 \ | |
| -outfmt 7 \ | |
| -query # put your query fasta here | |
| -db nt \ | |
| -out #.blastn |
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this script will launch a docker container for ncbi blast+ and build the prebuilt nt database, then blast a query against it.