Best Alignment tool of Denovo assembly Results.

Question

[clear.choi]

I have Denovo Assembly sequence from PacBio sequence.

It is around 2.9 GB size of sequences.

I'd like to know what is best alignment tool to analyze this data.

I am usually using this "blasr" to align HG19 to Sub reads. However, When I align HG19 to Denovo assembly results, It throwing the error. It looks like too large sequence to align it.

Could anyone know what is best practice to do it? I want to see and have bam file to visualize in IGV program.

Thank you in advance.

[GenoMax]

If you are trying to align 2.9 GB (genome sized) sequence to another reference genome (hg19) then you should look at a tool like LASTZ which is meant for aligning chromosome sized fragments.

[st.ph.n]

Bowtie and BWA are popular and widely used tools. Samtools will also become your friend. Example workflow.

[Brian Bushnell]

I don't think this really addresses the question, which is about whole-genome alignment. Neither bowtie nor bwa are suitable for that purpose. Mummer IS suitable but I don't think it produces bam files. If Blasr causes problems, you might try daligner.

Alternatively, you could just align the error-corrected reads to the human genome. That would be much simpler and likely more productive.

Answer 1

[colindaven]

You can probably achieve what you are trying to do easiest by aligning the pacbio contigs to the genome, not the genome to the contigs. Brian's comment is also very applicable, as is genomax's.

If you have really big contigs Bwa mem may still work, but use samtools and not Picard for converting and sorting contig size alignments from SAM to bam.