Hi Everyone,
I'm looking for software to map multiple mate reads to a reference genome (e.g. twenty mate reads with 100 to 500 bp gaps, each read is 5 bp). This is similar to Complete Genomics aligning four mate pairs, however, they've locked down their software.
I've looked into ClustalW and T-coffee, but I don't see a good way to specify the known gap position and gap constraint without it also applying to the reads themselves, i.e. I don't want the software to insert 100 bp gaps into the 5 mer read. I am new to bioinformatics, so I'm possibly missing something.
We've written a script in python using regex to map the mated reads, however, it doesn't handle mismatches or take quality into account.
Any suggestions on alignment software to map multiple mate pairs would be greatly appreciated.
Best regards,
-Sam
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...