.. _Bowtie2:

Bowtie2
=======

De acordo com a `página do Bowtie2 <https://github.com/BenLangmead/bowtie2>`_,
"*Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes*".


Versões Disponíveis
-------------------

* bowtie2/2.3.5.1


Submissão de Jobs Seriais
-------------------------

Crie um arquivo chamado, por exemplo, *submit_serial_jobs.sh*.

.. code-block:: bash

   #!/bin/bash
   #SBATCH -t 24:00:00

   export INPUT="run.sh reference reads eg1.sam"
   export OUTPUT="*"

   job-nanny ./run.sh

em que o script *run.sh* tem o seguinte conteúdo:

.. code-block:: bash

   #!/bin/bash
   module load bowtie2/2.3.5.1

   echo "====================[ Create index ]================================="
   bowtie2-build reference/lambda_virus.fa lambda_virus

   echo "====================[ Align ]================================="
   bowtie2 -x lambda_virus -U reads/reads_1.fq -S eg1.sam


Antes de submeter o job, deve-se tornar o script executável pelo comando

.. code-block:: bash

   chmod +x run.sh

Para submeter o processo, basta usar o comando:

.. code-block:: bash

   sbatch submit_serial_jobs.sh


Referências
-----------

Para informações adicionais sobre o software, consulte a `página do Bowtie2 <https://github.com/BenLangmead/bowtie2>`_.