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This article shows you how to understand the genome data analysis software SpeedSeq, which is concise and easy to understand, which will definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.

SpeedSeq is an open source software for analyzing genomic data variation. Its main functions are as follows

Alignments, sequence alignment

Variant detection, mutation detection

Functional annotation, functional annotation of the mutation site

The most important feature of the software is its rapidness. For 50x human genome data, the original fastq to vcf file only takes about 13 hours. The corresponding article is published on nature methods. The link is as follows.

Http://ucgd.genetics.utah.edu/wp-content/uploads/2015/08/nmeth.3505.pdf

The software is a complete pipeline that integrates a variety of software and can be used to detect the following genomic mutations

Germline and somatic mutations, using freebayes software to detect mutant microsites.

Structural variants, using lumpy-sv software to detect structural variation

The flow chart is as follows

The source code is saved on github with the following link

Https://github.com/hall-lab/speedseq

According to the function, the software is divided into the following five sub-modules

1. Align

The module compares the double-terminal sequenced fastq data to the reference genome, and then performs markduplicate, sort, index and other steps, which is consistent with the data preprocessing steps in the GATK process.

Speedseq align\

-R "@ RG\ tID:sample1\ tSM:sample1\ tLB:sample1"\

-t 10\

-o sample1\

Hg19.fa\

Sample1_R1.fastq.gz\

Sample1_R2.fastq.gz

Bwa software was used to compare the reference genome, then samblaster was used for markduplicate, and sambamba software was used for sort of bam files.

2. Var

This module is used to detect reproductive variation and input the bam file generated for the align module. The usage is as follows

Speedseq var\

-t 10\

Hg19.fa\

Sample1.bam

Freebayes software was used to detect reproductive variation, and the output file was VCF file.

3. Somatic

This module is used to detect somatic mutations and input the bam file generated by the align module, using the following

Speedseq somatic\

-t 10\

-o tumor\

Hg19.fa\

Normal.bam\

Tumor.bam

Using freebayes software to detect somatic mutation, paired tumor and normal samples are needed, and the output file is VCF file.

4. Sv

This module is used to detect structural variation, and the usage is as follows

Speedseq sv\

-o sample\

-B sample.bam\

-D sample.discordants.bam\

-S sample.splitters.bam\

-R hg19.fa\

-o sample\

-t 10

Lumpy-sv software is used to detect structural variation, and the output file is VCF file.

5. Realign

This module extracts the double-ended fastq sequence from the bam file and performs the same processing as the align module. The usage is as follows.

Speedseq realign\

-t 10\

-o sample\

Hg19.fa\

Sample.ba

The bam file is required to contain read group information, and the output file is the same as the align module. For the analysis of genome-wide data, the use of speedseq can greatly accelerate the processing speed.

The above content is how to understand the genome data analysis software SpeedSeq, have you learned the knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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