megamash

Documentation

Overview

Package megamash is an implementation of the megamash algorithm.

Megamash is an algorithm developed by Keoni Gandall to find templates from sequencing reactions. For example, you may have a pool of amplicons, and need to get a count of how many times each amplicon shows up in a given sequencing reaction.

Megamash takes all unique kmers of a given sequence among all other sequences in a pool, and uses those to distinguish how close a given target is to that particular sequence. This does not work if there are no unique kmers within a sequence: this can often happen in combinatorial libraries. For sequences like that, it is better to look to a different algorithm.

Index

• Variables
• func MatchesToJSON(matches []Match) (string, error)
• func StandardizeDNA(sequence string) string
• type Match
  • func JSONToMatches(jsonStr string) ([]Match, error)
• type MegamashMap
  • func NewMegamashMap(sequences []fasta.Record, kmerSize uint, kmerMinimalCount int, ...) (MegamashMap, error)
  • func (m *MegamashMap) Match(sequence string) []Match

Variables

var (
	DefaultKmerSize         uint    = 16
	DefaultMinimalKmerCount int     = 10
	DefaultScoreThreshold   float64 = 0.5
)

Functions

func MatchesToJSON

func MatchesToJSON(matches []Match) (string, error)

MatchesToJSON converts a slice of Match structs to a JSON string.

func StandardizeDNA

func StandardizeDNA(sequence string) string

StandardizeDNA returns the alphabetically lesser strand of a double stranded DNA molecule.

Types

type Match

type Match struct {
	Identifier string  `json:"identifier"`
	Score      float64 `json:"score"`
}

Match contains the identifier and score of a potential match to the searched sequence.

func JSONToMatches

func JSONToMatches(jsonStr string) ([]Match, error)

JSONToMatches converts a JSON string to a slice of Match structs.

type MegamashMap

type MegamashMap struct {
	Kmers                 map[string]string
	IdentifierToKmerCount map[string]int
	KmerSize              uint
	KmerMinimalCount      int
	Threshold             float64
}

func NewMegamashMap

func NewMegamashMap(sequences []fasta.Record, kmerSize uint, kmerMinimalCount int, threshold float64) (MegamashMap, error)

NewMegamashMap creates a megamash map that can be searched against.

func (*MegamashMap) Match

func (m *MegamashMap) Match(sequence string) []Match

Match matches a sequence to all the sequences in a megamash map.