Pileup to consensus sequence aligned to reference - Please help


Hi everyone,

I am new to bioinformatics and have made some really good progress in the last few weeks however I have found myself a little stuck and would greatly appreciate any help from the galaxy community.

I have taken some illumina MiSeq Fastq files, trimmed and quality checked them before aligning to multiple custom reference genomes. I have then created a pileup from the BAM file using generate pileup in SAMTools and the same set of reference genomes. I then used pileup to interval to try to get a consensus sequence however because my sequence is incomplete I get multiple chains of sequence. Is there a tool which will allow me to get a consensus fasta file from this pileup with Ns aligned to the area of the reference where there is no sequence data available?

Thanks in advance

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