Difference between revisions of "Applications/Mafft"

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(Created page with "__TOC__ ==Application Details== * Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. * Version: 2.2....")
 
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==Application Details==
 
==Application Details==
  
* Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.  
+
* Description: MAFFT is used to create multiple sequence alignments of amino acid or nucleotide sequences.
 
* Version: 2.2.9 (compiled with gcc)
 
* Version: 2.2.9 (compiled with gcc)
* Modules: bowtie2/gcc/2.2.9
+
* Modules: mafft/7.397
* Licence: Open source (Github)  
+
* Licence: Open source (Github)
  
 
==Usage Examples==
 
==Usage Examples==
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module load mafft/7.397
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[username@login01 ~]$ module add mafft/7.397
 
[username@login01 ~]$ mafft
 
[username@login01 ~]$ mafft
  
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module load mafft/7.397
+
[username@login01 ~]$ module add mafft/7.397
 
[username@login01 ~]$ mafft [arguments] input > output
 
[username@login01 ~]$ mafft [arguments] input > output
 
</pre>
 
</pre>
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[username@login01 ~]$ mafft --auto input > output
 
[username@login01 ~]$ mafft --auto input > output
 
</pre>
 
</pre>
 
 
 
 
 
 
---------------------------------------------------------------------
 
 
  MAFFT v7.397 (2018/Apr/16)
 
 
        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
 
        https://mafft.cbrc.jp/alignment/software/
 
---------------------------------------------------------------------
 
 
 
Input file? (fasta format)
 
@
 
  
 +
===Batch Job===
 +
<!-- ty NIH: https://hpc.nih.gov/apps/mafft.html -->
 +
<pre>
 +
#!/bin/bash
 +
#SBATCH J mafftjob
 +
#SBATCH N 1
 +
#SBATCH --exclusive
 +
#SBATCH --cpus-per-task=4
 +
#SBATCH -o %N-%j.out
 +
#SBATCH -e %N-%j.err
  
 +
module purge
 +
module load mafft/7.397
  
 +
mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile
 
</pre>
 
</pre>
  
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* [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT]
 
* [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT]
  
 
+
{{Modulepagenav}}
{|
 
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
|style="width:95%; border-width: 0" |
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]]
 
* [[General|General]]
 
* [[Training|Training]]
 
* [[Programming|Programming support]]
 
|-
 
|}
 

Latest revision as of 12:54, 17 November 2022

Application Details

  • Description: MAFFT is used to create multiple sequence alignments of amino acid or nucleotide sequences.
  • Version: 2.2.9 (compiled with gcc)
  • Modules: mafft/7.397
  • Licence: Open source (Github)

Usage Examples

Manual execution

[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft

---------------------------------------------------------------------

   MAFFT v7.397 (2018/Apr/16)

        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
        https://mafft.cbrc.jp/alignment/software/
---------------------------------------------------------------------


Input file? (fasta format)
@


Command line processing

[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft [arguments] input > output


An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites:

[username@login01 ~]$ mafft-linsi input > output


A fast option (FFT-NS-2) for a larger sequence alignment:

[username@login01 ~]$ mafft input > output


If not sure which option to use,

[username@login01 ~]$ mafft --auto input > output

Batch Job

#!/bin/bash
#SBATCH J mafftjob
#SBATCH N 1
#SBATCH --exclusive
#SBATCH --cpus-per-task=4
#SBATCH -o %N-%j.out
#SBATCH -e %N-%j.err

module purge
module load mafft/7.397

mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile

Further Information





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