Hi All,
I am working on BS-seq of one large genome size species, which have more than 20Gb.
I could not find any BS-seq aligner available which could be used to handle so large genome, such as BSmap, BSseeker, BRAT and so on.
Bismark looks okay, but very slow. and often aborted
"Processed 1000000 sequences so far
(ERR): bowtie2-align died with signal 9 (KILL)
Use of uninitialized value $alignment_score in concatenation (.) or string at /u/home/w/whfwind/project-mcdb/software/bismark_v0.13.0/bismark line 1999, <IN> line 228104432.
Use of uninitialized value $MD_tag in concatenation (.) or string at /u/home/w/whfwind/project-mcdb/software/bismark_v0.13.0/bismark line 1999, <IN> line 228104432.
Failed to extract alignment score () and MD tag ()!
(ERR): bowtie2-align died with signal 13 (PIPE) "
Anyone know which software is effective to handle so large genome.
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