- You can access available banks list and information (version, updates, location, and so on) by connecting on this page
- On cluster, databases path is /bank and you can also use the script bank_info.sh:
bank_info.sh -h
Usage :
-a : all available banks
-s : search bank (case insentitive,matching pattern)
-b : display bank's info
-h : help
Ex:
$ bank_info.sh -s uniref
uniref100
uniref50
uniref90
You can access the bank list available to be used within the NCBI Blast+ command line or the web site with the following command line:
ls /bank/blastdb/
Example:
module load bioinfo/ncbi-blast-2.10.0+
blastp -db nr -query path_to_fasta_file -evalue 0.001 -out path_to_output_file
You can access the bwa index list available with the following command line:
ls /bank/bwadb/
Example:
/bin/bash -c "bwa sampe /bank/bwadb/ensembl_homo_sapiens_genome < (bwa aln /bank/bwadb/ensembl_homo_sapiens_genome path_to_read1_fastq.gz_file) < (bwa aln /bank/bwadb/ensembl_homo_sapiens_genome path_to_read2_fastq.gz_file) path_to_read1_fastq.gz_file path_to_read2_fastq.gz_file | samtools view -bS - > path_to_output_bam";
You can access the bowtie index list available with the following command line:
ls /bank/bowtiedb/
Example:
bowtie /bank/bowtiedb/ensembl_homo_sapiens_genome -1 path_to_read1_fastq_file -2 path_to_read2_fastq_file | samtools view -bS - > path_to_output_bam
You can access the bowtie2 index list available with the following command line:
ls /bank/bowtie2db/
Example:
bowtie2 -x /bank/bowtie2db/ensembl_homo_sapiens_genome -1 path_to_read1_fastq_file -2 path_to_read2_fastq_file | samtools view -bS - > path_to_output_bam
You can access the Star index list available with the following command line:
ls /bank/STARdb/
To ask for a bank installation, please complete the following form: Bank installation