|Interface||Command line interface|
|Restrictions to use||None|
|Output format||SAM, tab-delimited text|
|License||GNU General Public License version 2.0|
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- person_outline Felix Krueger <>
If I really want to nitpick and find a negative point, I would say the parallelization is a bit of a hassle if you have limited resources, it's not as straightforward as setting the number of threads to use, you need some experimenting with parameters like --multicore and -p to find out how many actual cores (and RAM) are used for a typical run with your settings. Also, itás not the fastest tool in the world, for example BSMAP is said to be faster (especially in RRBS mode), but then again in side-by-side comparisons I always managed to map more reads with Bismark, and I think the speed is quite reasonable, I'm happy with it.
Overall Bismark is a wonderful tool, I can highly recommend it for any (RR)BS data analysis!