This file contains an example of the command launched to execute each of the tools. In these examples, the dataset was composed of reads whose length was 1600 nts  


Bismark:

/genome/ssd/src/bismark/bismark --bowtie2 -p 3 --path_to_bowtie /genome/ssd/src/bowtie2-2.1.0/ /genome/ssd/index_bowtie2/ /genome/datasets/datasets_2016_01_27/test_4M_1600nt_n3_r010.bwa.read1.fastq_convert.fastq --non_directional

(according to the Bismark user guide 4.0, 

"..BS-Seq libraries can be constructed so that all four different strands generated in the BS-PCR can and will end up in the sequencing library with roughly the same likelihood. In this case all four strands (OT, CTOT, OB, CTOB) can produce valid alignments and the library is called non-directional. Specifying ‘--non_directional’ instructs Bismark to use all four alignment outputs."

Note that -p 3 corresponds to 3 x 4 simultaneous alignments = 12 threads)

HPG-Methyl:

(time ../hpg-aligner bs -i /genome/ssd/index_bs_previous/ -f /genome/datasets/datasets_2016_01_27/test_4M_1600nt_n3_r010.bwa.read1.fastq_convert.fastq -o . --num-seeds 10 --seed-size 38 --min-seed-size 26 --min-cal-size 160 --max-distance-seeds 1600 --cpu-threads 12 --sw-min-score 0.8) > hpg_1600_010.txt 2> hpg_1600_010_time.txt

(this is the only case where the tool needs the user to explicitely use the appropriate parameter settings according to the length of the reads in the dataset.)

HPR-Methyl2:

(time ../hpg-aligner bs -i /genome/ssd/index_bs_previous/ -f /genome/datasets/datasets_2016_01_27/test_4M_1600nt_n3_r010.bwa.read1.fastq_convert.fastq -o .  --cpu-threads 12 ) > hpg_1600_010.txt 2> hpg_1600_010_time.txt