From: SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores
Definition | Notation | Example |
---|---|---|
set of nucleotides | â„• | â„• = {A, T, C, G} |
reference sequence | W | w = "T AGT CGAGG" |
read set | S | S = { "T AGT CG", "AGT CGA", "T CGAGG" } |
k-mer | α or α/ | α = "T AG", α/ = "CT A" |
positive k-mer | α + | α+ = "T AG" |
negative k-mer | α − | α− = "CT A" |
representative k-mer | α + | α+ = "T AG" |
k-molecule |
| = {"T AG", "CT A"} |
set of k-mers | ℤ(s, k) | ℤ("T AGT CG", 3) ={"TAG","AGT","GTC","TCG"} |
set of k-molecules | S(s, k) | ℤ("T AGT C", 3) = {{"T AG", "CT A"}, {"AGT ", "ACT "}, {"GT C", "GAC"}, {"T CG", "CGA"}} |