Difference between revisions of "Applications/Planatus"
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==Usage Examples== | ==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: | To load the module use the following command: | ||
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[username@login01 ~]$ module load planatus/1.2.24 | [username@login01 ~]$ module load planatus/1.2.24 | ||
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| − | Platanus_trim xxx_1.fastq xxx_2.fastq | + | [username@login01 ~]$ Platanus_trim xxx_1.fastq xxx_2.fastq |
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| − | 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: |
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| − | 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: |
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| − | 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: |
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Revision as of 09:44, 6 April 2017
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:
[username@login01 ~]$ module load 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
Further Information
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