三代相关软件

minimap2

软件下载地址
https://github.com/lh3/minimap2

作用：

Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database

mapping软件；可以比对DNA 和 RNA;

It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3–4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.查看原文

速度更快，准确率高

一个快速序列映射和校准程序查看原文

脚本:

/minimap/minimap2-2.16_x64-linux/minimap2 \
        -t 4 \
        -a \
        -x  map-ont \
        genome.fa file.fasta >fiel.sam

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sniffle

软件下载地址
https://github.com/fritzsedlazeck/Sniffles

Sniffles is a SV caller for long reads. It is mainly designed for PacBio reads, but also works on Oxford Nanopore reads.原文

用于sv的检测；可以使用 nanopore和pacbio的数据

脚本：

sniffles -m .bam -v file.vcf

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「三代组装」使用minimap+miniasm对nanopore进行基
https://www.jianshu.com/p/c91cb2ec5fc2