Gap filling single ended consensus

[MarleyC]

Hi All,

I'm quite new to the world of bioinformatics and I am currently work on building a baculovirus consensus sequence. I originally used CLC for most of my work but I find it has too many issues so I've opted to using open-source methods. I should also note that my data was produced using Ion Torrent with a 316 chip and 200bp chemistry.

Currently, I've mapped the sequence using BWA-mem to a reference and then pulled the consensus sequence using Samtools. Originally this inserted lots of 'N' in areas of low coverage. So I managed to split the sequence where the low coverage regions are and produced 11 contigs. My issue is, I want to gap fill these low coverage regions either from de novo assembly (I've done an assembly using ABySS) or filling from the reference sequence. I've looked at IMAGE2 and GapFIller but they seem to only work with single-end reads.

So my question is, how do I either fill these gaps from de novo assembly or reference fill?

Thanks!

[relipmoc]

You may try paparazzi, and use the contigs as the reference guide.

Hi All,

I'm quite new to the world of bioinformatics and I am currently work on building a baculovirus consensus sequence. I originally used CLC for most of my work but I find it has too many issues so I've opted to using open-source methods. I should also note that my data was produced using Ion Torrent with a 316 chip and 200bp chemistry.

Currently, I've mapped the sequence using BWA-mem to a reference and then pulled the consensus sequence using Samtools. Originally this inserted lots of 'N' in areas of low coverage. So I managed to split the sequence where the low coverage regions are and produced 11 contigs. My issue is, I want to gap fill these low coverage regions either from de novo assembly (I've done an assembly using ABySS) or filling from the reference sequence. I've looked at IMAGE2 and GapFIller but they seem to only work with single-end reads.

So my question is, how do I either fill these gaps from de novo assembly or reference fill?

Thanks!

[MarleyC]

You may try paparazzi, and use the contigs as the reference guide.

Thanks for the suggestion. Would this work for DNA viruses?

[Brian Bushnell]

Since you are using Ion Torrent data, I suggest mapping with BBMap as it is more accurate with calling indels than bwa-mem.