Use of Bowtie2 in NGS

Question

[p.prakash.saurabh]

hello everyone can anyone suggest me about the use of Bowtie2 is this tool could be used for contamination removal like adapter, tRNA, rRNA, unambiguous bases in NGS analysis.

[User 59]

Ever heard the expression 'use the right tool for the right job'? There are dedicated tools for adapter removal, rRNA screening etc. from NGS data, why would you necessarily want to use bowtie 2 for that? bowtie 2 is best used for aligning reads to a genome or transcriptome surely?

[WouterDeCoster]

He doesn't necessarily want to use Bowtie, he just wondered whether it was applicable. I can imagine that when starting now the myriad of tools available can be rather confusing. Although looking up published pipelines will learn you a lot...

[p.prakash.saurabh]

Thanks,just I wanted to know whether this tool can also be used to remove such contamination during Illumina based RNAseq analysis or only used to map reads to a reference genome.

Answer 1

[Medhat]

to remove adaptors and check quality ues one of those

NGS QC Toolkit
FASTX-Toolkit
cutadapt

[p.prakash.saurabh]

Thankyou so much medhat for this information

[WouterDeCoster]

I would like to add trimmomatic and prinseq to these, those have worked well for me.

Answer 2

[WouterDeCoster]

Bowtie2 is an aligner to map reads to a reference genome and is probably not suitable for the applications you describe, although it's rather unclear what exactly you aim to achieve.

[p.prakash.saurabh]

Thanks DeCoster, just I wanted to know whether this tool can also be used to remove such contamination during Illumina based RNAseq analysis or only used to map reads to a reference genome.

[WouterDeCoster]

As written by Daniel, there are dedicated tools for things like that. Googling should take you a long way. In general, exceptions exists, tools are good for one job and you'll just chain tools together to get the work done.