BWA alignment using de novo velvet contigs

[tracecakes]

Hi all,

-beware for a potentially stupid question-

I am using Velvet for the first time in hope to get a better alignment in a chromosome than just using my regular 100 bp paired end Illumina reads. I am doing this because the region appears to have a lot of repeats/gaps with normal BWA alignment.

Based on what I've read I am trying out different Velvet parameters to get the best N50 score.

I am using BWA to align the contigs back to the reference (don't know if this is the best thing to do) so I can see if the alignment has improved...I believe bwa bwasw is for longer single reads so I thought this would be appropriate.

However I am stuck on the bwa aln command.

bwa aln -t 4 canfam3.fasta contigs.fa > contigs.sai

It works fine for my contig.fa file that was produced with hash length 21, but when I try with contig.fa produced with hash length 31 I get an error:

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 159.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 94738 sequences have been processed.
[bsw2_aln] read 0 sequences (0 bp)...
[samopen] SAM header is present: 40 sequences.
[sam_read1] reference 'SN:X LN:123869142
' is recognized as '*'.
[main_samview] truncated file.

I have looked around but haven't found anything helpful, so does anyone have any ideas ? Or can someone suggest a better way of doing this?

Thanks in advance !

[Genomics101]

Hey there. Sorry you never got any answers here, especially since I have the same question! Please let me know if you figured it out.

[tracecakes]

Hi there Genomics101, it's been a while since I've worked on this but I could possibly help you out . What exactly is your question and the background to it ?

[Genomics101]

Hey there tracecakes, thanks for getting back to me. I want to align my contigs and/or scaffolds to a reference genome using BWA (or some other means) the same way I do it with the FASTQ reads. I am working on a genome that has a great deal of indel polymorphism - big ones, larger than can be easily captured using regular paired end sequencing. Thanks!

[tracecakes]

Have you tried the alignment with BWA/samtools or as you regularly do with your other FASTQs ? I was able to align my contigs.fa file using bwa bwasw (suitable for longer single reads like the contigs) and I could view the alignment using samtools tview. I still have not solved the hash length problem though.