FPS (Foundation Plant Services) repository
This repository contain scripts for analysis of Illumia data, including assembly, blast, and taxonomic identification
Installation requirements
This repository's scripts assume that the following programs are installed and placed in the Unix path:
- NCBI's BLAST with the NR BLAST database
- IDBA_UD
- samtools
- bwa
- cutadapt
- sickle
- R (plus these packages)
- taxize
- ggplot2
- seqinr
General usage
This repository should be placed in the Unix path. Most scripts can be run using
<script.sh> <data.file>
Details of the input data are included at the beginning of each script. Scripts will create directories where they are run with the results of the analysis. For example, if I run blastx.sh sample.001.fa in my home directory, I will get a folder called sample.001.fa.blast in my home directory, containing all the results.
Naming data and results
There is a naming scheme somewhere out there.
Scripts
###assemble.sh
$ assemble.sh <reads.fastq>
This script will take raw Illumina reads in fastq.gz format and cut adaptors (WGA) with cutadapt, remove low quality sequences with sickle, and assemble the reads with idba_ud.
###blastx.sh
$ blastx.sh <contig.fa>
This script will blastx against the NR database whatever sequences you give it. Output is in a tsv file.
###taxize_viruses.sh
$ taxize_viruses.sh <blast.tsv> <contigs.fa> <sequence description column number>
This script will return a list of the families each sequence is in, as well as a graph of the number of contigs in each family.
###csv-to-tsv.py
$ csv-to-tsv.py < in.csv > out.tsv
This script will convert a csv to a tsv. Useful for when data has commas in it.