PRINSEQ

-help or -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

-fastq

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.

FILE, stdin

-fasta

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.

FILE, stdin

-qual

Input file in QUAL format that contains the quality data

FILE

-fastq2

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.

FILE

-fasta2

or 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.

FILE

-params

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. Commends 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).

FILE

-si13

This option was replaced by option -phred64.

-phred64

Quality data in FASTQ file is in Phred+64 format (hhttp://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-

-out_format

Output format
1 (FASTA only), 2 (FASTA and QUAL), 3 (FASTQ), 4 (FASTQ and FASTA), 5 (FASTQ, FASTA and QUAL)

same as input

[1,2,3,4,5]

-out_good

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.

STRING, null, stdout

-out_bad

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: "-out_good stdout -out_bad null" will write data passing filters to STDOUT and data not passing any filter will be ignored

STRING, null, stdout

-log

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.

input name.log

STRING

-graph_data

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 log 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

input name.gd

STRING

-graph_stats

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 (Occurence 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

all

STRING

-qual_noscale

Use this option if all your sequences are shorter than 100bp and 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.)

-no_qual_header

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 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.

-min_len

Filter sequence shorter than min_len

INT

-max_len

Filter sequence longer than max_len

INT

-range_len

Filter sequence by length range. Multiple range values should be separated by comma without spaces.
Example: -range_len 50-100,250-300

STRING

-min_gc

Filter sequence with GC content below min_gc

INT [0..100]

-max_gc

Filter sequence with GC content above max_gc

INT [0..100]

-range_gc

Filter sequence by GC content range. Multiple range values should be separated by comma without spaces.

STRING

-min_qual_score

Filter sequence with at least one quality score below min_qual_score

INT

-max_qual_score

Filter sequence with at least one quality score above max_qual_score

INT

-min_qual_mean

Filter sequence with quality score mean below min_qual_mean

INT

-max_qual_mean

Filter sequence with quality score mean above max_qual_mean

INT

-ns_max_p

Filter sequence with more than ns_max_p percentage of Ns

INT [0..100]

-ns_max_n

Filter sequence with more than ns_max_n Ns

INT

-noniupac

Filter sequence with characters other than A, C, G, T or N

-seq_num

Only keep the first seq_num number of sequences (that pass all other filters)

INT

-derep

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)

INT

-derep_min

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).

2

INT [2..]

-lc_method

Method to filter low complexity sequences

[dust, entropy]

-lc_threshold

The threshold value used to filter sequences by sequence complexity. The dust method uses this as maximum allowed score and the entropy method as minimum allowed value.

INT [0..100]

-custom_params

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 occurence
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)

STRING

-trim_to_len

Trim all sequence from the 3'-end to result in sequence with this length

INT

-trim_left

Trim sequence at the 5'-end by trim_left positions

INT

-trim_right

Trim sequence at the 3'-end by trim_right positions

INT

-trim_left_p

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.

INT

-trim_right_p

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.

INT

-trim_tail_left

Trim poly-A/T tail with a minimum length of trim_tail_left at the 5'-end

INT

-trim_tail_right

Trim poly-A/T tail with a minimum length of trim_tail_right at the 3'-end

INT

-trim_ns_left

Trim poly-N tail with a minimum length of trim_ns_left at the 5'-end

INT

-trim_ns_right

Trim poly-N tail with a minimum length of trim_ns_right at the 3'-end

INT

-trim_qual_left

Trim sequence by quality score from the 5'-end with this threshold score

INT

-trim_qual_right

Trim sequence by quality score from the 3'-end with this threshold score

INT

-trim_qual_type

Type of quality score calculation to use

min

[min,mean,max,sum]

-trim_qual_rule

Rule to use to compare quality score to calculated value. Allowed options are lt (less than), gt (greater than) and et (equal to)

lt

[lt,gt,et]

-trim_qual_window

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.

1

INT

-trim_qual_step

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.

1

INT

-seq_case

Changes sequence character case to upper or lower case

[upper,lower]

-dna_rna

Convert sequence between DNA and RNA. Allowed options are "dna" (convert from RNA to DNA) and "rna" (convert from DNA to RNA).

[dna,rna]

-line_width

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.

60

INT

-rm_header

Remove the sequence header. This includes everything after the sequence identifier (which is kept unchanged)

-seq_id

Rename the sequence identifier. A counter is added to each identifier to assure its uniqueness

STRING

-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.