三代测序数据比对工具lra

论文

lra: A long read aligner for sequences and contigs

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009078

https://github.com/ChaissonLab/LRA

安装直接使用conda

conda install -c bioconda lra

参考序列构建索引

lra index -ONT pome_mt_potential.fa

比对

lra align -ONT pome_mt_potential.fa candidate_mt_longreads.fasta -t 8 -p s > output.sam

samtools sam转bam

samtools view -S -b -o output.bam output.sam

bam sort

samtools sort output.bam -o output.sorted.bam

提取map上的reads

参考 https://gist.github.com/davfre/8596159

samtools view -F 0x04 -b output.sorted.bam > output.aligned.bam