README.md

In WengLynn/shorten: Reduce the length of your sequences by removing the conserved sites.

shorten

Description: When you try to remove your conserved sites to reduce sequence length for further analysis such as calling adaptive mutations, I will recommend you to use it.

1.1 shorten_site (depends on tidyr and stringr)

To access it try:

 library(devtools)
 install_github("WengLynn/shorten")
 library(shorten)

To use it try:

shorten_site("filename.fasta","EPI_id",Start = 300, End = 29000,hm = 0)

parameters

key_pattern, the id of your refference sequence to label the location of every site.

lev, how many sites different to each other will be remain.

hm, how many difference sites will be treated as a difference. (default 0 as more than one difference.)

Start, the start site on refference.

End, the end site on refference.

Good Night

WengLynn/shorten documentation built on Jan. 3, 2022, 12:13 a.m.