Generate consensus from contig alignment to reference sequence
I have been trying to find a method to extract a consensus from de-novo assembled contigs against a reference genome. This is how I currently do this:
De-novo assemble the dataset. Identify sequence of interest in it. Run bowtie2/bwa mem to align the contigs against a reference genome of interest. Use igv to extract consensus.
Is there any other tool that can generate a consensus sequence from contigs and a reference genome?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How can I generate VCF file with two different assembled genome fasta?
written by kgwkk2 •
-
Mapping a small number of contigs to a reference subsequence
written by alexandru.bologa.marian •
-
Mapping metatranscriptomes to MAGs
written by pfchuckran •
-
Bacterial Seq Alignment
written by ravihansa82
-
RNASeq alignment visualisation
written by daewowo •
-
genome sequence from Spades output
written by BCArg
-
Mapping soft for de novo assembly
written by takoyaki
-
RNAseq consensus transcript sequence
written by Neuls •
-
How to align contigs from multiple species to a reference genome and then extract regions
written by fiona.lappin •
-
Assessing Quality And Accuracy Of De Novo Genome Assembly
written by a81526a •
Hi,
Have you looked at this post? It may help.