The fastest BS-seq data alignment tools and setting

Question

[Shicheng Guo]

Hi All,

Suppose I only want to make the fast methylation-seq data alignment. Which tools or which kind of setting can give me fastest alignment to get the bam file?

for example, my fastq file is 400G, I just hope to finish the alignment within one day. I can only use the maxmimu multiple-core=32

Now, I use bismark. it is fast not I still few it takes too long time. For bismark, -L 32 -N 0 will make it faster. but just quite limited.

Thanks.

Answer 1

[Devon Ryan]

Last I looked bsmap was probably the fastest BS-seq aligner. For 32-cores bwa-meth is also quite fast and will produce better quality alignments (unless things have changed with bsmap).