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Mira does it automatically, and so do most kmer based assemblers, they put coverage in terms of kmer coverage.
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Thanks nickloman,
I used IDBA-UD. I'll look into whether or not it will give me that output like you mentioned. Otherwise I will go ahead and re-align the reads and deal with it from there. I was just curious if there were already programs to do this, and it looks like the answer is that some assemblers do this automatically. Thanks for the answer!
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Which assembler did you use? Some will output this information in the FASTA header, or in a separate statistics file, in which case it is easy to write a script to extract the ones you want. Otherwise you will need to align the reads back to the contigs to get this info.
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Filtering Contigs by Coverage
Hi all,
I have a dataset where I assembled sequences into contigs and would now like to filter the contigs by coverage. My goal is to remove the contigs with low sequence coverage so that I can work only with those contigs with high coverage.
I am wondering if anybody knows if this is implemented in an existing sequence analysis program or something? I know I could write some code myself to do this, but I figured it was worth asking if anybody knows of this already existing? I haven't been able to find something that does this.
Thanks for your help!
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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