ART

ART

• Author: Dreycey Albin
• Date: 05/09/2019
• Updates: NAME (DATE): update descr; NAME (DATE): update descr,
• ART is used to generate illumina reads
• documentation (website):
• documentation (publication): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278762/

Installation

install gsl library

wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.5.tar.gz;
tar -zxvf gsl-2.5.tar.gz;
cd gsl-2.5;
./configure && make && make install;
cd ..;

MacOS installation

• install the binary in MacOS

wget https://www.niehs.nih.gov/research/resources/assets/docs/artsrcmountrainier2016.06.05macos.tgz

• open the tar

tar -zxvf artsrcmountrainier2016.06.05macos.tgz;
cd artsrcmountrainier2016.06.05macos

--> now do the "install gsl library"

./configure && make && make install

Linux installation

• install source code for Linux

wget https://www.niehs.nih.gov/research/resources/assets/docs/artsrcmountrainier2016.06.05linux.tgz;
cd art_src_MountRainier_MacOS/;

• open the tar

tar -zxvf artsrcmountrainier2016.06.05linux.tgz;
cd artsrcmountrainier2016.06.05linux;

--> now do the "install gsl library"

./configure && make && make install

Basic commands

INPUT

GENERAL INPUT INTO PROGRAM (files and commands)

OUTPUT

GENERAL OUTPUT FROM PROGRAM (files and commands)

Example_1

Input files

• Download an E. Coli genome from NCBI, use the

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz;
gzip -d GCF_000005845.2_ASM584v2_genomic.fna.gz;

Output files

• generates paired end reads and fastq files

paired_dat.sam 
paired_dat1.aln 
paired_dat1.fq 
paired_dat2.aln  
paired_dat2.fq

commands

./art_illumina -ss HS25 -sam -i GCF_000005845.2_ASM584v2_genomic.fna -p -l 150 -f 20 -m 200 -s 10 -o paired_dat;

Example_2

Input files

Output files

commands

# Paramaters

===== PARAMETERS =====
-1 --qprof1 the first-read quality profile
-2 --qprof2 the second-read quality profile
-amp --amplicon amplicon sequencing simulation
-c --rcount number of reads/read pairs to be generated per sequence/amplicon (not be used together with -f/--fcov)
-d --id the prefix identification tag for read ID
-ef  --errfree  indicate to generate the zero sequencing errors SAM file as well the regular one
NOTE: the reads in the zero-error SAM file have the same alignment positions
as those in the regular SAM file, but have no sequencing errors
-f --fcov the fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon
-h --help print out usage information
-i --in the filename of input DNA/RNA reference
-ir  --insRate  the first-read insertion rate (default: 0.00009)
-ir2 --insRate2 the second-read insertion rate (default: 0.00015)
-dr  --delRate  the first-read deletion rate (default:  0.00011)
-dr2 --delRate2 the second-read deletion rate (default: 0.00023)
-k --maxIndel the maximum total number of insertion and deletion per read (default: up to read length)
-l --len  the length of reads to be simulated
-m --mflen  the mean size of DNA/RNA fragments for paired-end simulations
-mp  --matepair indicate a mate-pair read simulation
-M  --cigarM  indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch
-nf  --maskN  the cutoff frequency of 'N' in a window size of the read length for masking genomic regions
NOTE: default: '-nf 1' to mask all regions with 'N'. Use '-nf 0' to turn off masking
-na  --noALN  do not output ALN alignment file
-o --out  the prefix of output filename
-p --paired indicate a paired-end read simulation or to generate reads from both ends of amplicons
NOTE: art will automatically switch to a mate-pair simulation if the given mean fragment size >= 2000
-q --quiet  turn off end of run summary
-qL  --minQ the minimum base quality score
-qU  --maxQ the maxiumum base quality score
-qs  --qShift the amount to shift every first-read quality score by
-qs2 --qShift2  the amount to shift every second-read quality score by
NOTE: For -qs/-qs2 option, a positive number will shift up quality scores (the max is 93)
that reduce substitution sequencing errors and a negative number will shift down
quality scores that increase sequencing errors. If shifting scores by x, the error
rate will be 1/(10^(x/10)) of the default profile.
-rs  --rndSeed  the seed for random number generator (default: system time in second)

NOTE: using a fixed seed to generate two identical datasets from different runs
-s --sdev the standard deviation of DNA/RNA fragment size for paired-end simulations.
-sam --samout indicate to generate SAM alignment file
-sp  --sepProf  indicate to use separate quality profiles for different bases (ATGC)
-ss  --seqSys The name of Illumina sequencing system of the built-in profile used for simulation

NOTE: sequencing system ID names are:
GA1 - GenomeAnalyzer I (36bp,44bp), GA2 - GenomeAnalyzer II (50bp, 75bp)
HS10 - HiSeq 1000 (100bp),  HS20 - HiSeq 2000 (100bp),  HS25 - HiSeq 2500 (125bp, 150bp)
HSXn - HiSeqX PCR free (150bp), HSXt - HiSeqX TruSeq (150bp), MinS - MiniSeq TruSeq (50bp)
MSv1 - MiSeq v1 (250bp),  MSv3 - MiSeq v3 (250bp),  NS50 - NextSeq500 v2 (75bp)

ART snakemake config file

#configfile: "art_snakeconfig.yaml"
genome_name = "GCF_000005845.2_ASM584v2_genomic"
rule art_simulator:
input:
"{genome_name}.fna"
output:
"{genome_name}_paired_dat.sam"
"{genome_name}_paired_dat1.aln"
"{genome_name}_paired_dat1.fq"
"{genome_name}_paired_dat2.aln"
"{genome_name}_paired_dat2.fq"
shell:
"./art_illumina -ss HS25 -sam -i {genome_name}.fna -p -l 150 -f 20 -m 200 -s 10 -o {genome_name}_paired_dat;"