Question: NGS bam file reference-guided assembly
gravatar for eitamarsaraf
5 weeks ago by
eitamarsaraf0 wrote:


I have some samples, where each has PE reads(150 bp length) of NGS in fastq format.

I already aligned them to the refseq with BWA.

I want to take N bases and do some kind of manipulation on them.

I thought to assemble the bam file, with the mutations, and in the gaps(where I don't have reads) fill it with the refseq.

do you know any reference-guided assembly that creates genomes to each sample, so I can take n bases from wherever I want?


alignment next-gen assembly • 133 views
ADD COMMENTlink modified 5 weeks ago by colindaven2.4k • written 5 weeks ago by eitamarsaraf0
gravatar for colindaven
5 weeks ago by
Hannover Medical School
colindaven2.4k wrote:

Do you mean something like consensus generation ?

Generating consensus sequence from bam file

I think you are also mixing alignment and assembly up. Please read basic NGS tutorials to understand this key difference.

ADD COMMENTlink written 5 weeks ago by colindaven2.4k

what is the diffrence from :

gatk4 FastaAlternateReferenceMaker -R $REFERENCE -O $CONSENSUS_FASTA -V $VCF

ADD REPLYlink modified 26 days ago • written 26 days ago by eitamarsaraf0

When you say reference guided assembly, a professional bioinformatician will think you are trying to do an assembly using tools such as Canu, Spades, etc, but using a reference genome to guide you.

What you are trying to do is use an alignment (BAM, VCF etc) and an existing Fasta to generate a consensus reference. Note : this is _not_ assembly.

But yes, GATK or samtools mutfa will likely do a good job on that. Beware insertions and deletions are inserted correctly.

ADD REPLYlink written 25 days ago by colindaven2.4k
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