Databanks

Training

Available bank list

• 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. You can also use the script bank_info.sh:

bank_info.sh -hUsage :
-a : all available banks
-s : search bank (case insentitive,matching pattern)
-b : display bank's info
-h : help

Example:

bank_info.sh -s unirefuniref100
uniref50
uniref90

NCBI blast+

You can access the bank list available to be used within the NCBI Blast+ command line or the website with the following command line:

ls /bank/blastdb/Anas_platyrhynchos.nal
Bos_taurus.nal
...

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

BWA index

You can access the bwa index list available with the following command line:

ls /bank/bwadb/Anas_platyrhynchos
Anas_platyrhynchos.amb
Anas_platyrhynchos.ann
Anas_platyrhynchos.bwt
Anas_platyrhynchos.pac
Anas_platyrhynchos.sa
Bos_taurus
Bos_taurus.amb
...

Example:

module load bioinfo/bwa/0.7.19module load bioinfo/samtools/1.21/bin/bash -c "bwa sampe /bank/bwadb/ensembl_homo_sapiens_genome < (bwa aln /bank/bwadb/ensembl_homo_sapiens_genome path/to/read1_file.fastq.gz) < (bwa aln /bank/bwadb/ensembl_homo_sapiens_genome path/to/read2_file.fastq.gz) path/to/read1_file.fastq.gz path/to/read2_file.fastq.gz | samtools view -bS - > path/to/output.bam";

Bowtie index

You can access the bowtie index list available with the following command line:

ls /bank/bowtiedb/Anas_platyrhynchos
Anas_platyrhynchos.1.ebwt
Anas_platyrhynchos.2.ebwt
Anas_platyrhynchos.3.ebwt
Anas_platyrhynchos.4.ebwt
Anas_platyrhynchos.rev.1.ebwt
Anas_platyrhynchos.rev.2.ebwt
Bos_taurus
Bos_taurus.1.ebwt
...

Example:

module load bioinfo/bowtie/1.2.1.1module load bioinfo/samtools/1.21bowtie /bank/bowtiedb/ensembl_homo_sapiens_genome -1 path/to/read1_file.fastq -2 path/to/read2_file.fastq | samtools view -bS - > path/to/output.bam

Bowtie2 index

You can access the bowtie2 index list available with the following command line:

ls /bank/bowtie2db/Bos_taurus
Bos_taurus.1.bt2
Bos_taurus.2.bt2
Bos_taurus.3.bt2
Bos_taurus.4.bt2
Bos_taurus.rev.1.bt2
Bos_taurus.rev.2.bt2
Capra_hircus
Capra_hircus.1.bt2
...

Example:

module load bioinfo/bowtie/2.5.4module load bioinfo/samtools/1.21bowtie2 -x /bank/bowtie2db/ensembl_homo_sapiens_genome -1 path/to/read1_file.fastq -2 path/to/read2_file.fastq | samtools view -bS - > path/to/output.bam

Star index

You can access the Star index list available with the following command line:

ls /bank/STARdb/Anas_platyrhynchos
Bos_taurus
Canis_lupus_familiaris
Capra_hircus
...

Ask for a bank

To ask for a bank installation, please complete the following form: Bank installation