pacbio bax.h5文件处理及ccs计算

Posted 2020-10-31 左筱弦

 1.NCBI文件格式如下：

 

2.格式转换

(1) bas.h5 -> ccs

source /share/nas2/genome/biosoft/smrtanalysis/2.3.0/smrtanalysis/current/etc/setup.sh

bash5tools.py --readType subreads --outType fasta /path/to/bas.h5

(2) bax.h5 -> ccs

需要各个文件进行转换并进行合并

source  /opt/smrtanalysis/install/smrtanalysis_2.3.0.140936/etc/setup.sh

ConsensusTools.sh CircularConsensus m161112_054131_42199_c101122602550000001823257305221784_s1_p0.3.bax.h5

 

3.文件格式

PacBio CCS (Circular Consensus Sequence) or RoI (Read of Insert) read

@<MovieName>/<ZMW_number>

（sequence）

 

PacBio CCS subread

@<MovieName> /<ZMW_number>/<subread-start>_<subread-end>