Benchmark with Bowtie2 - Githubissues

GZHoffie / approximate-string-matching

A repository of experimental code and benchmark for greedy/dynamic programming approximate string matching algorithms.

MIT License

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Open GZHoffie opened 2 years ago

GZHoffie commented 2 years ago

Study the code for alignment in bowtie2, and see how we can modify it to our greedy algorithm.

[ ] #12
[ ] Modify the two functions and fill score with penalty calculated by the greedy algorithm.
[ ] Adjust aligner_sw.cpp by deleting the backtracking steps.
[ ] Compile, debug, and run on example lambda_virus genome and reads.

GZHoffie commented 2 years ago

Let's record our findings in this issue.

LouieBHLu commented 2 years ago

Got it