Algorithm 1.

Pseudo code for FASTA conversion

input : Splice graph G

output : A compact FASTA file F that is correct and L-complete with regard to G

FUNCTION main(Graph G(V, E))

begin

Forall u ∈ V

If (Not(Visited(u))

F=DFS(u, EmptyString)

Print(F)

end

FUNCTION DFS(node u, str x)

begin

If (Visited(u))

F = DFSFiniteLength(u,x,L)

Else If (TERMINAL(u))

Visited(u) = True

$F=F\bigcup \{x+\mathrm{str}\left(u\right)\}$

Else

Visited(u) = True

x = x + str(u)

ForAll (outgoing neighbors v)

If (NotFirstEdge(u → v))

x = suffixL(x)

F=DFS(v,x)

Return(F)

end

input : Splice graph G, node u, str x, length l

output : All sequences of length l that start from node u

FUNCTION DFSFiniteLength(node u, str x, length l)

begin

If (length(u) > l)

$F=F\bigcup \{x+{\mathrm{prefix}}_l\left(\mathrm{str}\left(u\right)\right)\}$

Else If (TERMINAL(u))

$F=F\bigcup \{x+\mathrm{str}\left(u\right)\}$

Else

l = l - length(u)

x = x + str(u)

ForAll (outgoing neighbor v)

If (NotFirstEdge(u → v))

x = suffixL(x)

F=DFSFiniteLength(v,x,l)

Return(F)

end