autoReport: autoReport

In GuangchuangYu/skleid: State Key Lab of Emerging Infectious Diseases

Description

auto report sequence alignment and consensus sequence

Usage

autoReport(contig.folder, ref.folder, name.file, out.folder = "output",
  filter = FALSE, percentage = 1, markAmbiguous = TRUE)

Arguments

contig.folder	contig folder files in contig.folder should have name contains _S\d+[HNMP]+, or it will be move to unknown folder should contains for example: XXX_S111NA_454.fas, XXX_S111NA_Contigs.fna and XXX_S111NA_mira_delX.fasta
ref.folder	reference folder should contains files like XXX__S111NA_Ref.fas
name.file	name file
out.folder	output folder
filter	logical
percentage	filter percentage
markAmbiguous	makr ambiguous with * or not

Author(s)

ygc

GuangchuangYu/skleid documentation built on May 6, 2019, 9:03 p.m.