K Mer Counting Assignment

Tests

For this assignment, tests are not located with the assignment files. They are located in your src/test/java folder, not your hw6-src folder.

Files

Studio (in hw6-src)

• student.assignment.kmer.studio.StringHashMapKMerCounter (Test with student.assignment.kmer.studio.AStringHashMapTest)
• student.assignment.kmer.studio.StringConcurrentHashMapKMerCounter (Test with student.assignment.kmer.studio.BStringConcurrentHashMapTest)
• student.assignment.kmer.studio.SequenceSliceConcurrentHashMapKMerCounter (Test with student.assignment.kmer.studio.CSequenceSliceConcurrentHashMapTest)

Required Homework

• student.assignment.kmer.required.SequenceSlices (Test with student.assignment.kmer.required.DSequenceSlicesTest)
• student.assignment.kmer.required.LongConcurrentHashMapKMerCounter (Test with student.assignment.kmer.required.ELongConcurrentHashMapTest)
• student.assignment.kmer.required.IntArrayKMerCounter (Test with student.assignment.kmer.required.FIntArrayTest)
• student.assignment.kmer.required.AtomicIntegerArrayKMerCounter (Test with student.assignment.kmer.required.GAtomicIntegerArrayTest)

Optional (not extra credit)

student.assignment.kmer.fun.LongMatrixMapReducesqueKMerCounter (Test with student.assignment.kmer.fun.HLongMatrixMapReducesqueTest)

Extra Credit

student.assignment.kmer.extracredit.OpenEndedKMerCounter (Test with student.assignment.kmer.extracredit.IOpenEndedTest)

research

wikipedia article on k-mers

paper: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers (Jellyfish)

paper: Multiple comparative metagenomics using multiset k-mer counting

Collection of approaches to k-mer counting

Burrows–Wheeler transform

Significance of k-mer Counting