- -help |
-h
- Print the help message; ignore other arguments.
- -man
- Print the full documentation; ignore other arguments.
- -version
- Print program version; ignore other arguments.
- -verbose
- Prints status and info messages during processing.
- ***** INPUT OPTIONS *****
- -fastq
<file>
- Input file in FASTQ format that contains the sequence and quality data.
Use stdin instead of a file name to read from STDIN (-fasta stdin). This
can be useful to process compressed files using Unix pipes.
- -fasta
<file>
- Input file in FASTA format that contains the sequence data. Use stdin
instead of a file name to read from STDIN (-fastq stdin). This can be
useful to process compressed files using Unix pipes.
- -qual
<file>
- Input file in QUAL format that contains the quality data.
- -fastq2
<file>
- For paired-end data only. Input file in FASTQ format that contains the
sequence and quality data. The sequence identifiers for two matching
paired-end sequences in separate files can be marked by /1 and /2, or _L
and _R, or _left and _right, or must have the exact same identifier in
both input files. The input sequences must be sorted by their sequence
identifiers. Singletons are allowed in the input files.
- -fasta2
<file>
- For paired-end data only. Input file in FASTA format that contains the
sequence data. The sequence identifiers for two matching paired-end
sequences in separate files can be marked by /1 and /2, or _L and _R, or
_left and _right, or must have the exact same identifier in both input
files. The input sequences must be sorted by their sequence identifiers.
Singletons are allowed in the input files.
- -params
<file>
- Input file in text format that contains PRINSEQ parameters. Each parameter
should be specified on a new line and arguments should be separated by
spaces or tabs. Comments can be specified on lines starting with the #
sign. Can be combined with command line parameters. Parameters specified
on the command line will overwrite the arguments in the file (if
any).
- -si13
- This option was replaced by option -phred64.
- -phred64
- Quality data in FASTQ file is in Phred+64 format
(http://en.wikipedia.org/wiki/FASTQ_format#Encoding). Not required for
Illumina 1.8+, Sanger, Roche/454, Ion Torrent, PacBio data.
- -aa
- Input is amino acid (protein) sequences instead of nucleic acid (DNA or
RNA) sequences. Allowed amino acid characters:
ABCDEFGHIKLMNOPQRSTUVWYZXabcdefghiklmmopqrstuvwyzx*- and allowed nucleic
acid characters: ACGTURYKMSWBDHVNXacgturykmswbdhvnx-
The following options are ignored for -aa:
stats_dinuc,stats_tag,stats_ns,dna_rna
- ***** OUTPUT OPTIONS *****
- -out_format
<integer>
- To change the output format, use one of the following options. If not
defined, the output format will be the same as the input format.
1 (FASTA only), 2 (FASTA and QUAL), 3 (FASTQ), 4 (FASTQ and
FASTA), or 5 (FASTQ, FASTA and QUAL)
- -out_good
<string>
- By default, the output files are created in the same directory as the
input file containing the sequence data with an additional
"_prinseq_good_XXXX" in their name (where XXXX is replaced by
random characters to prevent overwriting previous files). To change the
output filename and location, specify the filename using this option. The
file extension will be added automatically (either .fasta, .qual, or
.fastq). For paired-end data, filenames contain additionally
"_1", "_1_singletons", "_2", and
"_2_singletons" before the file extension. Use "-out_good
null" to prevent the program from generating the output file(s) for
data passing all filters. Use "-out_good stdout" to write data
passing all filters to STDOUT (only for FASTA or FASTQ output files).
Example: use "file_passed" to generate the output
file file_passed.fasta in the current directory
- -out_bad
<string>
- By default, the output files are created in the same directory as the
input file containing the sequence data with an additional
"_prinseq_bad_XXXX" in their name (where XXXX is replaced by
random characters to prevent overwriting previous files). To change the
output filename and location, specify the filename using this option. The
file extension will be added automatically (either .fasta, .qual, or
.fastq). For paired-end data, filenames contain additionally
"_1" and "_2" before the file extension. Use
"-out_bad null" to prevent the program from generating the
output file(s) for data not passing any filter. Use "-out_bad
stdout" to write data not passing any filter to STDOUT (only for
FASTA or FASTQ output files).
Example: use "file_filtered" to generate the output
file file_filtered.fasta in the current directory
Example: "-out_good stdout -out_bad null" will write
data passing filters to STDOUT and data not passing any filter will be
ignored
- -log
<file>
- Log file to keep track of parameters, errors, etc. The log file name is
optional. If no file name is given, the log file name will be
"inputname.log". If the log file already exists, new content
will be added to the file.
- -graph_data
<file>
- File that contains the necessary information to generate the graphs
similar to the ones in the web version. The file name is optional. If no
file name is given, the file name will be "inputname.gd". If the
file already exists, new content will overwrite the file. Use
"-out_good null -out_bad null" to prevent generating any
additional outputs. (See below for more options related to the graph
data.)
The graph data can be used as input for the prinseq-graphs.pl
file to generate the PNG graph files or an HTML report file. If you have
trouble installing the required prinseq-graphs.pl modules or want to see
an output example report, upload the graph data file at:
http://edwards.sdsu.edu/prinseq/ -> Choose "Get Report"
- -graph_stats
<string>
- Use this option to select what statistics should be calculated and
included in the graph_data file. This is useful if you e.g. do not need
sequence complexity information, which requires a lot of computation.
Requires to have graph_data specified. Default is all selected.
Allowed option are (separate multiple by comma with no
spaces): ld (Length distribution), gc (GC content distribution), qd
(Base quality distribution), ns (Occurrence of N), pt (Poly-A/T tails),
ts (Tag sequence check), aq (Assembly quality measure), de (Sequence
duplication - exact only), da (Sequence duplication - exact + 5'/3'), sc
(Sequence complexity), dn (Dinucleotide odds ratios, includes the PCA
plots)
Example use: -graph_stats ld,gc,qd,de
- -qual_noscale
- Use this option if all your sequences are shorter than 100bp as they do
not require to scale quality data to 100 data points in the graph. By
default, quality scores of sequences shorter than 100bp or longer than
100bp are fit to 100 data points. (To retrieve this information and
calculate the graph data would otherwise require to parse the data two
times or store all the quality data in memory.)
- In order to reduce the file size, this option will generate an empty
header line for the quality data in FASTQ files. Instead of +header, only
the + sign will be output. The header of the sequence data will be left
unchanged. This option applies to FASTQ output files only.
- -exact_only
- Use this option to check for exact (forward and reverse) duplicates only
when generating the graph data. This allows one to keep the memory
requirements low for large input files and is faster. This option will
automatically be applied when using -derep options 1 and/or 4 only.
Specify option -derep 1 or -derep 4 if you do not want to apply both at
the same time.
- -seq_id_mappings
<file>
- Text file containing the old and new (specified with -seq_id) identifiers
for later reference. This option is useful if e.g. a renamed sequence has
to be identified based on the new sequence identifier. The file name is
optional. If no file name is given, the file name will be
"inputname_prinseq_good.ids" (only good sequences are renamed).
If a file with the same name already exists, new content will overwrite
the old file. The text file contains one sequence identifier pair per
line, separated by tabs (old-tab-new). Requires option -seq_id.
- ***** FILTER OPTIONS *****
- -min_len
<integer>
- Filter sequence shorter than min_len.
- -max_len
<integer>
- Filter sequence longer than max_len.
- -range_len
<string>
- Filter sequence by length range. Multiple range values should be separated
by comma without spaces.
Example: -range_len 50-100,250-300
- -min_gc
<integer>
- Filter sequence with GC content below min_gc.
- -max_gc
<integer>
- Filter sequence with GC content above max_gc.
- -range_gc
<string>
- Filter sequence by GC content range. Multiple range values should be
separated by comma without spaces.
Example: -range_gc 50-60,75-90
- -min_qual_score
<integer>
- Filter sequence with at least one quality score below min_qual_score.
- -max_qual_score
<integer>
- Filter sequence with at least one quality score above max_qual_score.
- -min_qual_mean
<integer>
- Filter sequence with quality score mean below min_qual_mean.
- -max_qual_mean
<integer>
- Filter sequence with quality score mean above max_qual_mean.
- -ns_max_p
<integer>
- Filter sequence with more than ns_max_p percentage of Ns.
- -ns_max_n
<integer>
- Filter sequence with more than ns_max_n Ns.
- -noniupac
- Filter sequence with characters other than A, C, G, T or N.
- -seq_num
<integer>
- Only keep the first seq_num number of sequences (that pass all other
filters).
- -derep
<integer>
- Type of duplicates to filter. Allowed values are 1, 2, 3, 4 and 5. Use
integers for multiple selections (e.g. 124 to use type 1, 2 and 4). The
order does not matter. Option 2 and 3 will set 1 and option 5 will set 4
as these are subsets of the other option.
1 (exact duplicate), 2 (5' duplicate), 3 (3' duplicate), 4
(reverse complement exact duplicate), 5 (reverse complement 5'/3'
duplicate)
- -derep_min
<integer>
- This option specifies the number of allowed duplicates. If you want to
remove sequence duplicates that occur more than x times, then you would
specify x+1 as the -derep_min values. For examples, to remove sequences
that occur more than 5 times, you would specify -derep_min 6. This option
can only be used in combination with -derep 1 and/or 4 (forward and/or
reverse exact duplicates). [default : 2]
- -lc_method
<string>
- Method to filter low complexity sequences. The current options are
"dust" and "entropy". Use "-lc_method dust"
to calculate the complexity using the dust method.
- -lc_threshold
<integer>
- The threshold value (between 0 and 100) used to filter sequences by
sequence complexity. The dust method uses this as maximum allowed score
and the entropy method as minimum allowed value.
- -custom_params
<string>
- Can be used to specify additional filters. The current set of possible
rules is limited and has to follow the specifications below. The custom
parameters have to be specified within quotes (either ' or ").
Please separate parameter values with a space and separate new
parameter sets with semicolon (;). Parameters are defined by two values:
(1) the pattern (any combination of the letters "ACGTN"),
(2) the number of repeats or percentage of occurrence Percentage values
are defined by a number followed by the %-sign (without space). If no
%-sign is given, it is assumed that the given number specifies the
number of repeats of the pattern.
Examples: "AAT 10" (filters out sequences containing
AATAATAATAATAATAATAATAATAATAAT anywhere in the sequence), "T
70%" (filters out sequences with more than 70% Ts in the sequence),
"A 15" (filters out sequences containing AAAAAAAAAAAAAAA
anywhere in the sequence), "AAT 10;T 70%;A 15" (apply all
three filters)
- ***** TRIM OPTIONS *****
- -trim_to_len
<integer>
- Trim all sequence from the 3'-end to result in sequence with this
length.
- -trim_left
<integer>
- Trim sequence at the 5'-end by trim_left positions.
- -trim_right
<integer>
- Trim sequence at the 3'-end by trim_right positions.
- -trim_left_p
<integer>
- Trim sequence at the 5'-end by trim_left_p percentage of read length. The
trim length is rounded towards the lower integer (e.g. 143.6 is rounded to
143 positions). Use an integer between 1 and 100 for the percentage
value.
- -trim_right_p
<integer>
- Trim sequence at the 3'-end by trim_right_p percentage of read length. The
trim length is rounded towards the lower integer (e.g. 143.6 is rounded to
143 positions). Use an integer between 1 and 100 for the percentage
value.
- -trim_tail_left
<integer>
- Trim poly-A/T tail with a minimum length of trim_tail_left at the
5'-end.
- -trim_tail_right
<integer>
- Trim poly-A/T tail with a minimum length of trim_tail_right at the
3'-end.
- -trim_ns_left
<integer>
- Trim poly-N tail with a minimum length of trim_ns_left at the 5'-end.
- -trim_ns_right
<integer>
- Trim poly-N tail with a minimum length of trim_ns_right at the
3'-end.
- -trim_qual_left
<integer>
- Trim sequence by quality score from the 5'-end with this threshold
score.
- -trim_qual_right
<integer>
- Trim sequence by quality score from the 3'-end with this threshold
score.
- -trim_qual_type
<string>
- Type of quality score calculation to use. Allowed options are min, mean,
max and sum. [default: min]
- -trim_qual_rule
<string>
- Rule to use to compare quality score to calculated value. Allowed options
are lt (less than), gt (greater than) and et (equal to). [default:
lt]
- -trim_qual_window
<integer>
- The sliding window size used to calculate quality score by type. To stop
at the first base that fails the rule defined, use a window size of 1.
[default: 1]
- -trim_qual_step
<integer>
- Step size used to move the sliding window. To move the window over all
quality scores without missing any, the step size should be less or equal
to the window size. [default: 1]
- ***** REFORMAT OPTIONS *****
- -seq_case
<string>
- Changes sequence character case to upper or lower case. Allowed options
are "upper" and "lower". Use this option to remove
soft-masking from your sequences.
- -dna_rna
<string>
- Convert sequence between DNA and RNA. Allowed options are "dna"
(convert from RNA to DNA) and "rna" (convert from DNA to
RNA).
- -line_width
<integer>
- Sequence characters per line. Use 0 if you want each sequence in a single
line. Use 80 for line breaks every 80 characters. Note that this option
only applies to FASTA output files, since FASTQ files store sequences
without additional line breaks. [default: 60]
- Remove the sequence header. This includes everything after the sequence
identifier (which is kept unchanged).
- -seq_id
<string>
- Rename the sequence identifier. A counter is added to each identifier to
assure its uniqueness. Use option -seq_id_mappings to generate a file
containing the old and new identifiers for later reference.
Example: "mySeq_10" will generate the IDs (in FASTA
format) >mySeq_101, >mySeq_102, >mySeq_103, ...
- ***** SUMMARY STATISTIC OPTIONS *****
- The summary statistic values are written to STDOUT in the form:
"parameter_name statistic_name value" (without the quotes). For
example, "stats_info reads 10000" or "stats_len max
500". Only one statistic is written per line and values are separated
by tabs.
If you specify any statistic option, no other output will be
generated. To preprocess data, do not specify a statistics option.
- -stats_info
- Outputs basic information such as number of reads (reads) and total bases
(bases).
- -stats_len
- Outputs minimum (min), maximum (max), range (range), mean (mean), standard
deviation (stddev), mode (mode) and mode value (modeval), and median
(median) for read length.
- -stats_dinuc
- Outputs the dinucleotide odds ratio for AA/TT (aatt), AC/GT (acgt), AG/CT
(agct), AT (at), CA/TG (catg), CC/GG (ccgg), CG (cg), GA/TC (gatc), GC
(gc) and TA (ta).
- -stats_tag
- Outputs the probability of a tag sequence at the 5'-end (prob5) and 3'-end
(prob3) in percentage (0..100). Provides the number of predefined MIDs
(midnum) and the MID sequences (midseq, separated by comma, only provided
if midnum > 0) that occur in more than 34/100 (approx. 3%) of the
reads.
- -stats_dupl
- Outputs the number of exact duplicates (exact), 5' duplicates (5), 3'
duplicates (3), exact duplicates with reverse complements (exactrevcom)
and 5'/3' duplicates with reverse complements (revcomp), and total number
of duplicates (total). The maximum number of duplicates is given under the
value name with an additional "maxd" (e.g. exactmaxd or
5maxd).
- -stats_ns
- Outputs the number of reads with ambiguous base N (seqswithn), the maximum
number of Ns per read (maxn) and the maximum percentage of Ns per read
(maxp). The maxn and maxp value are not necessary from the same
sequence.
- -stats_assembly
- Outputs the N50, N90, etc contig sizes. The Nxx contig size is a weighted
median that is defined as the length of the smallest contig C in the
sorted list of all contigs where the cumulative length from the largest
contig to contig C is at least xx% of the total length (sum of contig
lengths).
- -stats_all
- Outputs all available summary statistics.
- ***** ORDER OF PROCESSING *****
- The available options are processed in the following order:
seq_num, trim_left, trim_right, trim_left_p, trim_right_p,
trim_qual_left, trim_qual_right, trim_tail_left, trim_tail_right,
trim_ns_left, trim_ns_right, trim_to_len, min_len, max_len, range_len,
min_qual_score, max_qual_score, min_qual_mean, max_qual_mean, min_gc,
max_gc, range_gc, ns_max_p, ns_max_n, noniupac, lc_method, derep,
seq_id, seq_case, dna_rna, out_format