Aligning two genomes in fastq.gz

Question

[sukesh1411]

Hi

I would like to find the variants among two different genomes (both are paired end reads). I removed the low quality reads for two genomes using sickle tool. Now i got two paired end output files from sickle which are in fastq.gz format. Can anyone suggest me the tool for aligningtwo different genomes. I am searching for an option in bwa but i did not find it.. or can i concatenate paired end fastq files of one genome into one file and then convert it to fasta file to create an index file.

Thanks

[Medhat]

you can use lastz or Mauve and its input is fasta file ,after assemble your reads

or you can align the read of one genome to the other genome and then detect variant using SAMtools, GATK or freebayes

Answer 1

[Chris Cole]

A fastq file is not a genome. It is a set of short high-throughput sequencing reads which derive from a DNA or RNA sample library.

In order to find variants, fastq reads need to be aligned to a reference genome and then variants called with a tool suitable for your species. This needs to be done separately for each of your two 'genomes' (samples?). What species are your samples?

[sukesh1411]

Thank you sir. I am working on two different varieties of oryza sativa.

[Chris Cole]

Are they related to either of the known strains: japonica and indica? If they are, you can use the most similar one as a reference and do variant calling against that.

Otherwise you're heading down the road of whole genome assembly, which for a species like rice is a huge project taking an experienced person several months to do well.

[sukesh1411]

Its related to japonica and i will do variant calling against it. Thank you sir.