FastD Download

1. Introduction

FastD is a comprehensive tool to detect insecticide resistance-associated nucleic acids changes from next-generation sequencing data. There are two web services, FastD_TR and FastD_MR , which were developed to detect two kind of nucleic acids changes associated with insecticide resistance. For some personal confidential data to be tested, the stand-alone software were also available and can be operated on Linux and Windows system.

2. Prerequisites

2.1 Third-party software packages for FastD.

- R (version 3.4.0 or later versions) and R packages (ggplot2, ggseqlogo and DESeq2)
- Python (version 2.6 or later versions)
- Bowtie2 (version 2.2.9 or later version)

2.2 Unpack FastD

$ tar -xzvf FastD_v1.0_linux.tar.gz
$ cd FastD_v1.0_linux

3. Running FastD

Usage: FastD_TR

FastD_TR.pl  [options]*  -s [species]  -r [targets]  -i [input]  

-s/--species	The name of Species you want to detect,connection name with "_". Such as,use "Plutella_xylostella" instead of "Plutella xylostella".
-r/--target	Mutations in four insecticide targets were collected. Resistance to a insecticide may be associated with mutations in its target. Before running the software, please choose appropriate target.
-i/--input	The alignment sam file generated by aligning RNA-Seq data to target gene.

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Options:

-o/--out	The prefix for the output data.
-v/--version	Print version information and quit.
-h/--help	print this usage message.

Examples:

perl  FastD_TR.pl  -s  Plutella_xylostella  -r  RyR  VGSC  nAChR  AChE  -i  *.sam  -o  *

Input:
The raw reads in RNA-Seq data are used to map with target gene sequences using bowtie2. The result sam file was submitted as input data.

Output:

*.csv
result_mutation_scaned*
*.png
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*.csv
The FastD_TR result including the mutations in targets and their frequency.
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result_mutation_scaned*
The codons in reads corresponding each mutation site is listed in the *.txt file.
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*.png
The figure display the amino acid changes in all potential mutation sites.

Usage: FastD_MR

FastD_MR.pl  -s [species]  -e [enzyme]  -1 [input1]  -2 [input2]  

-s/--species	The name of Species you want to detect,connection name with "_". Such as,use "Plutella_xylostella" instead of "Plutella xylostella".
-e/--enzyme	The overexpression of detoxifying enzyme genes may be associated with insecticide resistance.To detected resistance, you should first choose specific enzymes.
-1	The input alignment files of sensitive samples.
-2	The input alignment files of resistant samples.

options:

-o/--out	The prefix for the output data.
-v/--version	Print version information and quit.
-h/--help	print this usage message.

Examples:

perl  FastD_MR.pl  -s  Plutella_xylostella  -e  P450 GST CCE -1  sensitive_1.sam  sensitive_2.sam  sensitive_3.sam  -2  resistant_1.sam  resistant_2.sam  resistant_3.sam  -o  result

Input:
The raw reads in RNA-Seq data are used to map to specific detoxifying enzyme genes of selected species using bowtie2. The result sam files was submitted as input data.

Output:

*.csv
The result of FastD_MR lists the detoxifying enzyme genes which are selected to be the potential resistance causal genes.