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gregorysprenger/blast-plus-biopython

By gregorysprenger

•Updated almost 4 years ago

Docker container that contains: NCBI Blast+, Python, and Biopython

Image
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gregorysprenger/blast-plus-biopython repository overview

⁠BLAST+ and Biopython

This image implements:

and the Dockerfiles can be found on github⁠.

⁠Example analysis:

Get test data:

mkdir -p data
cd data

# Download test data
wget -nv https://raw.githubusercontent.com/nf-core/test-datasets/44bd1eb9292b34a78c41a423805c14b63f2da56c/data/delete_me/e_coli_k12_16s.fna

Build BLASTn 16S database:

update_blastdb.pl 16S_ribosomal_RNA
tar -zxvf 16S_ribosomal_RNA.tar.gz

Run BLASTn on e_coli data using 16S database:

blastn \
    -task blastn \
    -db 16S_ribosomal_RNA \
    -query e_coli_k12_16s.fna \
    -outfmt "6 sseqid pident length mismatch gapopen gaps ssciname" \
    -out pos_blast.tsv

Further analysis of BLASTn ouptut can be analyzed via Biopython.

Tag summary

Content type

Image

Digest

sha256:dc6a4cd2d…

Size

891.1 MB

Last updated

almost 4 years ago

docker pull gregorysprenger/blast-plus-biopython:2.9.0-py2.7-1.6.8