bioref

BLAST databases

MSI maintains the entire NCBI BLAST sequence database, which are currently 34 separate databases. Table 1 below shows the names of these BLAST databases, a brief description of their contents, their database format version, the full path to their location on our system, and the versions of NCBI BLAST software that they are compatible with. 

Latest BLAST databases are located within:

/common/bioref/blast/latest/

If you are loading BLAST software 2.12.0 or greater using “module load” on our system, the latest bioref BLAST databases are automatically loaded in your environment, so there is no need to specify the full path to the database - providing only the database name (in column 1 of Table 1) for the database argument will suffice. Please note that the BLAST databases in bioref are in dbV5 format, so they will not work with any versions of BLAST software older than 2.12.0+. 

BLAST databases and their locations in bioref

BLAST Update Schedule

January

April

July

October

The bioref BLAST databases will be updated quarterly on the months listed in the update schedule and kept for 2 years. If needed, you can find older versions of the BLAST databases within the /common/bioref/blast/ folder, named by their month and year they were downloaded (e.g. “blast_update_04_2023” refers to the April 2023 update). 
 

ENSEMBL databases

The genomes and gene annotations for all organisms from ENSEMBL, except bacteria, are stored in /common/bioref/ensembl/. In addition to storing the genomes (FASTA format) and gene annotations (GFF and GTF formats), we also provide pre-built genome indices for BWA, HISAT2, Bowtie, Bowtie2, Samtools, NCBI_toolkit, and Picard. Note: Protein sequences and transcript sequences (FASTA format) corresponding to the genes in the ENSEMBL GTF/GFFs are not provided.

Latest ENSEMBL databases are located within:

/common/bioref/ensembl/

Organisms are organized into directories based on their kingdom (plants, metazoan, fungi, etc), except “main” which contains model organisms and vertebrates. 

ENSEMBL Directory Structure

Within each “genus_species” directory, you will find the following subdirectories:

Software Versions/Commands used for genomic sequence indexing

ENSEMBL Update Schedule

ENSEMBL databases will be updated annually in January and will be kept for 4 years. If needed, you can find older versions of the ENSEMBL databases within the ENSEMBL folder labeled by the month and year (e.g. “ensembl_update_01_2023”).

Genome Indexes for Single-Cell Software

10X Genomics Cellranger References

Parse Biosciences split-pipe References

/common/bioref/splitpipe_parse
Contains pre-built split-pipe indices for human (hg38) and mouse (mm10) genome for demultiplexing single-cell libraries from Parse Biosciences. Indices were built with parse-pipeline v1.5.0.

Kraken2/Bracken Database

/common/bioref/kraken2/
Contains two pre-made metagenomics indices downloaded from the following link: https://benlangmead.github.io/aws-indexes/k2. The suffix indicates the date of release (standard) or release number (silva). 

Microbiome Databases

/common/bioref/microbiome/
Contains dada2_taxonomy_references (see https://benjjneb.github.io/dada2/training.html for more information)
and reference databases from the various biobakery_workflows (see https://huttenhower.sph.harvard.edu/biobakery_workflows/ for more information).