Difference between revisions of "Applications/Planatus"
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'''Platanus''' is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. | '''Platanus''' is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. | ||
| − | To load the module | + | To load the module using the following command: |
<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 | + | [username@login01 ~]$ module add planatus/1.2.24 |
</pre> | </pre> | ||
| − | If you want to treat the raw data, you can trim adaptor sequences and low quality regions from paired-end sequences as follows: | + | If you want to treat the raw data, you can trim adaptor sequences and low-quality regions from paired-end sequences as follows: |
<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;"> | ||
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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 ~]$ | + | [username@login01 ~]$ Platanus gap_close –o Pxut –c Pxut_scaffold.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq -t 16 2> gapclose.log |
</pre> | </pre> | ||
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* [http://platanus.bio.titech.ac.jp/ http://platanus.bio.titech.ac.jp/] | * [http://platanus.bio.titech.ac.jp/ http://platanus.bio.titech.ac.jp/] | ||
| + | ==Navigation== | ||
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* [[Main_Page|Home]] | * [[Main_Page|Home]] | ||
| − | * [[Applications|Application support]] | + | * [[Applications|Application support]] * |
* [[General|General]] | * [[General|General]] | ||
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* [[Programming|Programming support]] | * [[Programming|Programming support]] | ||
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Latest revision as of 13:10, 13 October 2022
Application Details
- Description: Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
- Version: 1.2.24
- Modules: planatus/1.2.24
- Licence: Free for academic use
Usage Examples
Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
To load the module using the following command:
[username@login01 ~]$ module add planatus/1.2.24
If you want to treat the raw data, you can trim adaptor sequences and low-quality regions from paired-end sequences as follows:
[username@login01 ~]$ Platanus_trim xxx_1.fastq xxx_2.fastq
Platanus_internal_trim program and you can obtain the trimmed internal adaptor sequences, adaptor sequences, and low quality regions named xxx_1.fastq.int_trimmed and xxx_2.fastq.int_trimmed.
[username@login01 ~]$ Platanus_internal_trim xxx_1.fastq xxx_2.fastq
Contig assembling from the trimmed fastq sequences, the contig assembling procedure should be performed at the beginning. An example command would be:
[username@login01 ~]$ Platanus assemble –o Pxut –f ./DRR02167[34]_[12].fastq –t 16 –m 128 2> assemble.log
After contig assembling, you can perform scaffolding using paired-end or mate-paired sequences. An example command would be:
[username@login01 ~]$ Platanus scaffold –o Pxut –c Pxut_contig.fa –b Pxut_contigBubble.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq -t 16 2> scaffold.log
Gap-closing - you can then perform gap-closing against scaffolding results. An example command would be:
[username@login01 ~]$ Platanus gap_close –o Pxut –c Pxut_scaffold.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq -t 16 2> gapclose.log