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+cutadapt version 4.4
+
+Copyright (C) 2010-2022 Marcel Martin <marcel.martin@scilifelab.se>
+
+cutadapt removes adapter sequences from high-throughput sequencing reads.
+
+Usage:
+    cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
+
+For paired-end reads:
+    cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
+
+Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
+characters are supported. All reads from input.fastq will be written to
+output.fastq with the adapter sequence removed. Adapter matching is
+error-tolerant. Multiple adapter sequences can be given (use further -a
+options), but only the best-matching adapter will be removed.
+
+Input may also be in FASTA format. Compressed input and output is supported and
+auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
+standard input/output. Without the -o option, output is sent to standard output.
+
+Citation:
+
+Marcel Martin. Cutadapt removes adapter sequences from high-throughput
+sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
+http://dx.doi.org/10.14806/ej.17.1.200
+
+Run "cutadapt --help" to see all command-line options.
+See https://cutadapt.readthedocs.io/ for full documentation.
+
+Options:
+  -h, --help            Show this help message and exit
+  --version             Show version number and exit
+  --debug               Print debug log. Use twice to also print DP matrices
+  -j CORES, --cores CORES
+                        Number of CPU cores to use. Use 0 to auto-detect.
+                        Default: 1
+
+Finding adapters:
+  Parameters -a, -g, -b specify adapters to be removed from each read (or from
+  R1 if data is paired-end. If specified multiple times, only the best
+  matching adapter is trimmed (but see the --times option). Use notation
+  'file:FILE' to read adapter sequences from a FASTA file.
+
+  -a ADAPTER, --adapter ADAPTER
+                        Sequence of an adapter ligated to the 3' end (paired
+                        data: of the first read). The adapter and subsequent
+                        bases are trimmed. If a '$' character is appended
+                        ('anchoring'), the adapter is only found if it is a
+                        suffix of the read.
+  -g ADAPTER, --front ADAPTER
+                        Sequence of an adapter ligated to the 5' end (paired
+                        data: of the first read). The adapter and any preceding
+                        bases are trimmed. Partial matches at the 5' end are
+                        allowed. If a '^' character is prepended ('anchoring'),
+                        the adapter is only found if it is a prefix of the read.
+  -b ADAPTER, --anywhere ADAPTER
+                        Sequence of an adapter that may be ligated to the 5' or
+                        3' end (paired data: of the first read). Both types of
+                        matches as described under -a and -g are allowed. If the
+                        first base of the read is part of the match, the
+                        behavior is as with -g, otherwise as with -a. This
+                        option is mostly for rescuing failed library
+                        preparations - do not use if you know which end your
+                        adapter was ligated to!
+  -e E, --error-rate E, --errors E
+                        Maximum allowed error rate (if 0 <= E < 1), or absolute
+                        number of errors for full-length adapter match (if E is
+                        an integer >= 1). Error rate = no. of errors divided by
+                        length of matching region. Default: 0.1 (10%)
+  --no-indels           Allow only mismatches in alignments. Default: allow both
+                        mismatches and indels
+  -n COUNT, --times COUNT
+                        Remove up to COUNT adapters from each read. Default: 1
+  -O MINLENGTH, --overlap MINLENGTH
+                        Require MINLENGTH overlap between read and adapter for
+                        an adapter to be found. Default: 3
+  --match-read-wildcards
+                        Interpret IUPAC wildcards in reads. Default: False
+  -N, --no-match-adapter-wildcards
+                        Do not interpret IUPAC wildcards in adapters.
+  --action {trim,retain,mask,lowercase,none}
+                        What to do if a match was found. trim: trim adapter and
+                        up- or downstream sequence; retain: trim, but retain
+                        adapter; mask: replace with 'N' characters; lowercase:
+                        convert to lowercase; none: leave unchanged. Default:
+                        trim
+  --rc, --revcomp       Check both the read and its reverse complement for
+                        adapter matches. If match is on reverse-complemented
+                        version, output that one. Default: check only read
+
+Additional read modifications:
+  -u LEN, --cut LEN     Remove LEN bases from each read (or R1 if paired; use -U
+                        option for R2). If LEN is positive, remove bases from
+                        the beginning. If LEN is negative, remove bases from the
+                        end. Can be used twice if LENs have different signs.
+                        Applied *before* adapter trimming.
+  --nextseq-trim 3'CUTOFF
+                        NextSeq-specific quality trimming (each read). Trims
+                        also dark cycles appearing as high-quality G bases.
+  -q [5'CUTOFF,]3'CUTOFF, --quality-cutoff [5'CUTOFF,]3'CUTOFF
+                        Trim low-quality bases from 5' and/or 3' ends of each
+                        read before adapter removal. Applied to both reads if
+                        data is paired. If one value is given, only the 3' end
+                        is trimmed. If two comma-separated cutoffs are given,
+                        the 5' end is trimmed with the first cutoff, the 3' end
+                        with the second.
+  --quality-base N      Assume that quality values in FASTQ are encoded as
+                        ascii(quality + N). This needs to be set to 64 for some
+                        old Illumina FASTQ files. Default: 33
+  --poly-a              Trim poly-A tails
+  --length LENGTH, -l LENGTH
+                        Shorten reads to LENGTH. Positive values remove bases at
+                        the end while negative ones remove bases at the
+                        beginning. This and the following modifications are
+                        applied after adapter trimming.
+  --trim-n              Trim N's on ends of reads.
+  --length-tag TAG      Search for TAG followed by a decimal number in the
+                        description field of the read. Replace the decimal
+                        number with the correct length of the trimmed read. For
+                        example, use --length-tag 'length=' to correct fields
+                        like 'length=123'.
+  --strip-suffix STRIP_SUFFIX
+                        Remove this suffix from read names if present. Can be
+                        given multiple times.
+  -x PREFIX, --prefix PREFIX
+                        Add this prefix to read names. Use {name} to insert the
+                        name of the matching adapter.
+  -y SUFFIX, --suffix SUFFIX
+                        Add this suffix to read names; can also include {name}
+  --rename TEMPLATE     Rename reads using TEMPLATE containing variables such as
+                        {id}, {adapter_name} etc. (see documentation)
+  --zero-cap, -z        Change negative quality values to zero.
+
+Filtering of processed reads:
+  Filters are applied after above read modifications. Paired-end reads are
+  always discarded pairwise (see also --pair-filter).
+
+  -m LEN[:LEN2], --minimum-length LEN[:LEN2]
+                        Discard reads shorter than LEN. Default: 0
+  -M LEN[:LEN2], --maximum-length LEN[:LEN2]
+                        Discard reads longer than LEN. Default: no limit
+  --max-n COUNT         Discard reads with more than COUNT 'N' bases. If COUNT
+                        is a number between 0 and 1, it is interpreted as a
+                        fraction of the read length.
+  --max-expected-errors ERRORS, --max-ee ERRORS
+                        Discard reads whose expected number of errors (computed
+                        from quality values) exceeds ERRORS.
+  --discard-trimmed, --discard
+                        Discard reads that contain an adapter. Use also -O to
+                        avoid discarding too many randomly matching reads.
+  --discard-untrimmed, --trimmed-only
+                        Discard reads that do not contain an adapter.
+  --discard-casava      Discard reads that did not pass CASAVA filtering (header
+                        has :Y:).
+
+Output:
+  --quiet               Print only error messages.
+  --report {full,minimal}
+                        Which type of report to print: 'full' or 'minimal'.
+                        Default: full
+  --json FILE           Dump report in JSON format to FILE
+  -o FILE, --output FILE
+                        Write trimmed reads to FILE. FASTQ or FASTA format is
+                        chosen depending on input. Summary report is sent to
+                        standard output. Use '{name}' for demultiplexing (see
+                        docs). Default: write to standard output
+  --fasta               Output FASTA to standard output even on FASTQ input.
+  -Z                    Use compression level 1 for gzipped output files
+                        (faster, but uses more space)
+  --info-file FILE      Write information about each read and its adapter
+                        matches into FILE. See the documentation for the file
+                        format.
+  -r FILE, --rest-file FILE
+                        When the adapter matches in the middle of a read, write
+                        the rest (after the adapter) to FILE.
+  --wildcard-file FILE  When the adapter has N wildcard bases, write adapter
+                        bases matching wildcard positions to FILE. (Inaccurate
+                        with indels.)
+  --too-short-output FILE
+                        Write reads that are too short (according to length
+                        specified by -m) to FILE. Default: discard reads
+  --too-long-output FILE
+                        Write reads that are too long (according to length
+                        specified by -M) to FILE. Default: discard reads
+  --untrimmed-output FILE
+                        Write reads that do not contain any adapter to FILE.
+                        Default: output to same file as trimmed reads
+
+Paired-end options:
+  The -A/-G/-B/-U/-Q options work like their lowercase counterparts, but are
+  applied to R2 (second read in pair)
+
+  -A ADAPTER            3' adapter to be removed from R2
+  -G ADAPTER            5' adapter to be removed from R2
+  -B ADAPTER            5'/3 adapter to be removed from R2
+  -U LENGTH             Remove LENGTH bases from R2
+  -Q [5'CUTOFF,]3'CUTOFF
+                        Quality-trimming cutoff for R2. Default: same as for R1
+  -p FILE, --paired-output FILE
+                        Write R2 to FILE.
+  --pair-adapters       Treat adapters given with -a/-A etc. as pairs. Either
+                        both or none are removed from each read pair.
+  --pair-filter {any,both,first}
+                        Which of the reads in a paired-end read have to match
+                        the filtering criterion in order for the pair to be
+                        filtered. Default: any
+  --interleaved         Read and/or write interleaved paired-end reads.
+  --untrimmed-paired-output FILE
+                        Write second read in a pair to this FILE when no adapter
+                        was found. Use with --untrimmed-output. Default: output
+                        to same file as trimmed reads
+  --too-short-paired-output FILE
+                        Write second read in a pair to this file if pair is too
+                        short.
+  --too-long-paired-output FILE
+                        Write second read in a pair to this file if pair is too
+                        long.