Databanks

You can access available banks list and information (version, updates, location, and so on) by connecting on this page.


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:

blastall -p blastn -d nt -i path_to_fasta_file -e 0.001 -o 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