On this site you can find the source code of the simulation program sbs_ffcm_simul.c to simulate the distribution of sequence length for sequencing by synthesis (SBS), and compare the simulation results with the analytical results. The program is written in C programming language. To compile the program, use something like this (different platforms/compilers differ slightly): gcc -Wall -o sbs_ffcm_simul sbs_ffcm_simul.c I also include two compiled binary (executable) files, one for 32-bit computers (sbs_ffcm_simul_32), one for 64-bit computers (sbs_ffcm_simul_64). To use the program: ./sbs_ffcm_simul -f -r -a -b -c -d -A a0,a1,... -B b0,b1,... -C c0,c1,... -D d0,d1,... The parameters are: -f: number of flow cycles -r: number of simulations -a: nucleotide context probability of "a" -b: nucleotide context probability of "b" -c: nucleotide context probability of "c" -d: nucleotide context probability of "d" -A: a list of nucleotide incorporation probabilities of nucleotide "a" -B: a list of nucleotide incorporation probabilities of nucleotide "b" -C: a list of nucleotide incorporation probabilities of nucleotide "c" -D: a list of nucleotide incorporation probabilities of nucleotide "d" For example, ./sbs_ffcm_simul -f 100 -r 200000 -a 0.3333 -b 0.0909 -c 0.4329 -d 0.1429 -A .1090909091,.5,.3,.09090909091 -B .3166666667,.25,.3333333333,.1 -C .646031 7460,.1428571429,.1,.1111111111 -D .425,.2,.25,.125 Yong Kong Yale University yong.kong@yale.edu