Applications/Planatus - Revision history

Pysdlb at 13:10, 13 October 2022

2022-10-13T13:10:47Z

Pysdlb at 13:35, 24 May 2019

2019-05-24T13:35:09Z

Pysdlb at 14:08, 7 June 2018

2018-06-07T14:08:19Z

Pysdlb at 10:04, 6 April 2017

2017-04-06T10:04:50Z

Pysdlb: Pysdlb moved page Application/Planatus to Applications/Planatus without leaving a redirect

2017-04-06T09:53:52Z

Pysdlb moved page Application/Planatus to Applications/Planatus without leaving a redirect

Pysdlb: Pysdlb moved page Planatus to Application/Planatus without leaving a redirect

2017-04-06T09:50:25Z

Pysdlb moved page Planatus to Application/Planatus without leaving a redirect

Pysdlb at 09:45, 6 April 2017

2017-04-06T09:45:16Z

Pysdlb at 09:44, 6 April 2017

2017-04-06T09:44:49Z

Pysdlb: Created page with "TOC ==Application Details== * Description: Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from mas..."

2017-04-06T09:42:01Z

Created page with "__TOC__ ==Application Details== * Description: Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from mas..."

New page

__TOC__

==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 use the following command:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@login01 ~]$ module load planatus/1.2.24

</pre>

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;">
Platanus_trim xxx_1.fastq xxx_2.fastq
</pre>

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.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ Platanus_internal_trim xxx_1.fastq xxx_2.fastq
</pre>

Contig assembling from the trimmed fastq sequences, the contig assembling procedure should be performed at the beginning. An example command would be:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ Platanus assemble –o Pxut –f ./DRR02167[34]_[12].fastq –t 16 –m 128 2> assemble.log
</pre>

After contig assembling, you can perform scaffolding using paired-end or mate-paired sequences. An example command would be:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[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
</pre>

Gap-closing - you can then perform gap-closing against scaffolding results. An example command would be:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[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>

==Further Information==

* [http://platanus.bio.titech.ac.jp/ http://platanus.bio.titech.ac.jp/]

{|
|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]]
|-
|}

@@ Line 12: / Line 12: @@
 '''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 use the following command:
+To load the module using the following command:
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
@@ Line 18: / Line 18: @@
 </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;">

@@ Line 56: / Line 56: @@
 * [http://platanus.bio.titech.ac.jp/ http://platanus.bio.titech.ac.jp/]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 15: / Line 15: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load planatus/1.2.24
+[username@login01 ~]$ module add planatus/1.2.24
 </pre>

@@ Line 47: / Line 47: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[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
+[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>

← Older revision	Revision as of 09:53, 6 April 2017
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← Older revision	Revision as of 09:50, 6 April 2017
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@@ Line 10: / Line 10: @@
 ==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.
+'''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 use the following command:
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@login01 ~]$ module load planatus/1.2.24
 </pre>
@@ Line 23: / Line 21: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-Platanus_trim xxx_1.fastq xxx_2.fastq
+[username@login01 ~]$ Platanus_trim xxx_1.fastq xxx_2.fastq
 </pre>
@@ Line 32: / Line 30: @@
 </pre>
-Contig assembling from the trimmed fastq sequences, the contig assembling procedure should be performed at the beginning. An example command would be:
+'''Contig assembling''' from the trimmed fastq sequences, the contig assembling procedure should be performed at the beginning. An example command would be:
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
@@ Line 39: / Line 37: @@
-After contig assembling, you can perform scaffolding using paired-end or mate-paired sequences. An example command would be:
+After contig assembling, you can perform '''scaffolding''' using paired-end or mate-paired sequences. An example command would be:
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
@@ Line 46: / Line 44: @@
-Gap-closing - you can then perform gap-closing against scaffolding results. An example command would be:
+'''Gap-closing''' - you can then perform gap-closing against scaffolding results. An example command would be:
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">