Hi,
From documentatioon it appears that ABySS only can output contigs and scaffolds in fasta. Is there a way to get more detailed assemblies, which list reads that compose contigs? My feeling is that this task is restricted to de novo assemblers that can output sam, bam and other more informative assembly formats. I used 454 newbler, but it discards reads shorter that 75 nt or so (Illumina datasets).
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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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