Provided by: art-nextgen-simulation-tools_20160605+dfsg-3_amd64 bug


       art_illumina - Simulation of Illumina sequencers


       ART  is  a set of simulation tools to generate synthetic next-generation sequencing reads.
       ART simulates sequencing reads by mimicking real sequencing process with  empirical  error
       models or quality profiles summarized from large recalibrated sequencing data.

       art_illumina can be used for Simulation of Illumina sequencers


       art_illumina  [options]  -sam  -i  <seq_ref_file>  -l <read_length> -f <fold_coverage> -ss
       <sequencing_system> -o <outfile_prefix>

       art_illumina [options] -sam -i  <seq_ref_file>  -l  <read_length>  -f  <fold_coverage>  -o

       art_illumina  [options]  -sam  -i  <seq_ref_file> -l <read_length> -c <total_num_reads> -o

       art_illumina [options] -sam -i  <seq_ref_file>  -l  <read_length>  -f  <fold_coverage>  -m
       <mean_fragsize> -s <std_fragsize> -o <outfile_prefix>

       art_illumina  [options]  -sam  -i  <seq_ref_file> -l <read_length> -c <total_num_reads> -m
       <mean_fragsize> -s <std_fragsize> -o <outfile_prefix>


       -1   --qprof1
              the first-read quality profile

       -2   --qprof2
              the second-read quality profile

       -amp --amplicon amplicon sequencing simulation

       -c   --rcount
              total number of reads/read pairs to be generated  [per  amplicon  if  for  amplicon
              simulation](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

       -nf  --maskN
              the cutoff frequency of 'N' in a window size of the read length for masking genomic

              NOTE: default: '-nf 1' to mask all regions with  'N'.  Use  '-nf  0'  to  turn  off

       -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

              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

       -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 - Genome Analyzer I, GA2 - Genome Analyzer II

       HS10 - HiSeq 1000, HS20 - HiSeq 2000, HS25 - HiSeq 2500, MS - MiSeq

       -M  --cigarM
              indicate to use CIGAR 'M' instead of '=/X' for alignment match/mismatch


       * 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


       1) single-end read simulation

              art_illumina -sam -i reference.fa -l 150 -ss HS25 -f 10 -o single_dat

       2) paired-end read simulation

              art_illumina  -sam  -i  reference.fa  -p  -l  150  -ss  HS25  -f 20 -m 200 -s 10 -o

       3) mate-pair read simulation

              art_illumina -sam -i reference.fa -mp -l 50 -f 20 -m 2500 -s 50 -o matepair_dat

       4) amplicon sequencing simulation with 5' end single-end reads

              art_illumina -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 -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 -amp -mp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_mate_dat

       7) generate an extra SAM file with zero-sequencing errors for a paired-end read simulation

              art_illumina -ef -i reference.fa -p -l 50 -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

       9) turn off the masking of genomic regions with unknown nucleotides 'N'

              art_illumina  -nf  0  -sam  -i  reference.fa  -p  -l  50  -f  20  -m  200  -s 10 -o

       10) masking genomic regions with >=5 'N's within the read length 50

              art_illumina -nf 5  -sam  -i  reference.fa  -p  -l  50  -f  20  -m  200  -s  10  -o


       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.