生物信息学流程也可以是perl开发

Posted 2021-04-17 生信技能树

最近很多生物信息学流程框架出来了，主要是商业公司或者个别爱好者在学习，大部分朋友都还是shell脚本，一步步衔接即可。

不过今天看文章发现还是有人用perl在串流程，非常的眼熟，就推荐一下：

这个流程包含的步骤：

• perform quality control on FastQ files (using FastQC)

• align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)

• perform quality control on generated BAM files (using Picard)

• count reads in features (using HTSeq-count)

• normalize read counts (using DESeq)

• calculate RPKMs (using edgeR)

• perform DE analysis for standard designs (using DESeq2)

• variant calling, filtering and annotation

代码超千行，满满的都是回忆：

结尾：