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YEAT: Your Everyday Assembly Tool
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Handling single-end short reads #36

Closed danejo3 closed 10 months ago

danejo3 commented 1 year ago

Currently, YEAT is unable to handle single-end short reads. While single-end data is quite rare to come across these days, having the capability to handle both single and pair-ends reads would be a great addition to YEAT.

After doing some research, I've learned that single-end and paired-end reads have their own purposes.

Single-end reads are: 1) Cheaper 2) Quicker to compile 3) Great way to profile and get a count of certain regions of the DNA 4) The rudimentary way of obtaining sequencing data

Paired-end reads are: 1) More expensive 2) Slower to compile 3) Produces more data 4) Gives additional positional information for a read (highly needed when doing de novo genome assembly) 5) Easier to resolve the structure of the genome

Going to start with with spades.py --s and branch out to other assemblers currently used in YEAT.

danejo3 commented 10 months ago

This issue thread is handled in #50