目錄
ART基因序列產生器簡介
官網1.
軟件下載2.
相關論文3.
ART使用
軟件配置
tar zxvf artbingreatsmokymountains041716linux64tgz.tgz
cd art_bin_GreatSmokyMountains/
#art_illumina=~/congmin/software/art_bin_GreatSmokyMountains/art_illumina參數設置
zhoukr@bsn001:~/congmin/software/art_bin_GreatSmokyMountains$ art_illumina
====================ART====================
ART_Illumina (2008-2016)
Q Version 2.5.1 (Apr 17, 2016)
Contact: Weichun Huang <[email protected]>
-------------------------------------------
===== USAGE =====
art_illumina [options] -ss <sequencing_system> -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -o <outfile_prefix>
art_illumina [options] -ss <sequencing_system> -sam -i <seq_ref_file> -l <read_length> -c <num_reads_per_sequence> -o <outfile_prefix>
art_illumina [options] -ss <sequencing_system> -sam -i <seq_ref_file> -l <read_length> -f <fold_coverage> -m <mean_fragsize> -s <std_fragsize> -o <outfile_prefix>
art_illumina [options] -ss <sequencing_system> -sam -i <seq_ref_file> -l <read_length> -c <num_reads_per_sequence> -m <mean_fragsize> -s <std_fragsize> -o <outfile_prefix>
===== 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)
-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)
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)
===== NOTES =====
* ART by default selects a built-in quality score profile according to the read length specified for the run.
* For single-end simulation, ART requires input sequence file, outputfile prefix, read length, and read count/fold coverage.
* For paired-end simulation (except for amplicon sequencing), ART also requires the parameter values of
the mean and standard deviation of DNA/RNA fragment lengths
===== EXAMPLES =====
1) single-end read simulation
art_illumina -ss HS25 -sam -i reference.fa -l 150 -f 10 -o single_dat
2) paired-end read simulation
art_illumina -ss HS25 -sam -i reference.fa -p -l 150 -f 20 -m 200 -s 10 -o paired_dat
3) mate-pair read simulation
art_illumina -ss HS10 -sam -i reference.fa -mp -l 100 -f 20 -m 2500 -s 50 -o matepair_dat
4) amplicon sequencing simulation with 5' end single-end reads
art_illumina -ss GA2 -amp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_5end_dat
5) amplicon sequencing simulation with paired-end reads
art_illumina -ss GA2 -amp -p -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_pair_dat
6) amplicon sequencing simulation with matepair reads
art_illumina -ss MSv1 -amp -mp -sam -na -i amp_reference.fa -l 150 -f 10 -o amplicon_mate_dat
7) generate an extra SAM file with zero-sequencing errors for a paired-end read simulation
art_illumina -ss HSXn -ef -i reference.fa -p -l 150 -f 20 -m 200 -s 10 -o paired_twosam_dat
8) reduce the substitution error rate to one 10th of the default profile
art_illumina -i reference.fa -qs 10 -qs2 10 -l 50 -f 10 -p -m 500 -s 10 -sam -o reduce_error
9) turn off the masking of genomic regions with unknown nucleotides 'N'
art_illumina -ss HS20 -nf 0 -sam -i reference.fa -p -l 100 -f 20 -m 200 -s 10 -o paired_nomask
10) masking genomic regions with >=5 'N's within the read length 50
art_illumina -ss HSXt -nf 5 -sam -i reference.fa -p -l 150 -f 20 -m 200 -s 10 -o paired_maskN5
使用實例
代碼
zhoukr@bsn001:~/congmin/software/art_bin_GreatSmokyMountains$ art_illumina -ss HS20 -i GRCH38chr1L3556522.fna -l 100 -f 20 -o G38L100F20Nhs20結果
zhoukr@bsn001:~/congmin/software/art_bin_GreatSmokyMountains$ art_illumina -ss HS20 -i GRCH38chr1L3556522.fna -l 100 -f 20 -o G38L100F20Nhs20
====================ART====================
ART_Illumina (2008-2016)
Q Version 2.5.1 (Apr 17, 2016)
Contact: Weichun Huang <whduke@gmail.com>
-------------------------------------------
還在運行結果文件
zhoukr@bsn001:~/congmin/software/art_bin_GreatSmokyMountains$ ll
total 9443836
drwxrwxr-x 2 hadoop hadoop 4096 6月 2 23:10 ./
drwxrwxr-x 6 hadoop hadoop 4096 6月 2 22:59 ../
-rw-rw-r-- 1 hadoop hadoop 4635232124 6月 2 23:11 G38L100F20Nhs20.aln
-rw-rw-r-- 1 hadoop hadoop 4347022003 6月 2 23:11 G38L100F20Nhs20.fq
-rw-r--r-- 1 hadoop hadoop 252513055 6月 2 23:00 GRCH38chr1L3556522.fna