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
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