加载中…从三代数据中组装细胞器（线粒体和叶绿体基因组）
(2017-09-22 17:52:07) | 分类： 生物信息学 |
1:参考文献：
Soorni A, Haak D, Zaitlin D, et al. Organelle_PBA, a pipeline for
assembling chloroplast and mitochondrial genomes from PacBio DNA
sequencing data[J]. BMC genomics, 2017, 18(1): 49.
2:网站：https://github.com/aubombarely/Organelle_PBA
4:至于软件怎么样，还没有测过，正在进行时，软件安装：
git clone https://github.com/aubombarely/Organelle_PBA.git
5:软件依赖：
BioPerl -- (used to process sequences)
Seqtk -- (used to change formats fastq/fasta)
BlastN -- (used for the assembly, find origin and check circularity)
BlasR -- (used to get the organelle related reads)
Samtools -- (used to process BlasR output for coverage)
Bedtools -- (used to calculate coverage for the repeat analysis)
Sprai -- (used for de-novo assembly)
WGS-Assembler -- (used for de-novo asembly by Sprai)
SSPACE-Long -- (used for the rescaffolding)
6:添加环境变量
export LD_LIBRARY_PATH=glibc/glibc-v2.14/lib:$LD_LIBRARY_PATH
export BLASR_PATH=/home/Softwares/smrtanalysis_2.3.0/current/analysis/bin/
export SAMTOOLS_PATH=/home/fanyucai/software/samtools/samtools-v1.4/bin/
export SPRAI_PATH=/home/fanyucai/software/sprai/sprai-v0.9.9.23/bin
export BLAST_PATH=/home/fanyucai/software/blast+/ncbi-blast-2.6.0+/bin/
export CA_PATH=/home/fanyucai/software/Celera_Assembler/wgs-8.3rc2/Linux-amd64/bin/ export SSPACELONG_PATH=/home/fanyucai/software/SSPACE/SSPACE-LongRead_v1-1/
export BEDTOOLS_PATH=/home/fanyucai/software/bedtools/bedtools2/bin/
7:脚本运行
OrganelleRef_PBA -t fasta -i pacbio.fasta -r ref.fasta -o mitochondrial/ -b -nproc=40 -s num_threads=40
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