Concatenate multiple FASTA/FASTQ files, in a similar way of the GNU cat utility.

Usage: cat [options] [<inputfile> ...]

Concatenate multiple FASTA or FASTQ files.

Options:
  -k, --skip STEP        Print one sequence every STEP [default: 0]
  --skip-first INT       Skip the first INT records [default: -1]
  --jump-to STR          Start from the record after the one named STR
                         (overrides --skip-first)
  --print-last           Print the name of the last sequence to STDERR (Last:NAME)

Sequence name:
  -p, --prefix STRING    Rename sequences with prefix + incremental number
  -z, --strip-name       Remove the original sequence name
  -a, --append STRING    Append this string to the sequence name [default: ]
  --sep STRING           Sequence name fields separator [default: _]

  -b, --basename         Prepend file basename to the sequence name (before prefix)
  --split CHAR           Split basename at this char [default: .]
  --part INT             After splitting the basename, take this part [default: 1]
  --basename-sep STRING  Separate basename from the rest with this [default: _]
  --zero-pad INT         Zero pad the counter to INT digits [default: 0]

Sequence comments:
  -s, --strip-comments   Remove original sequence comments
  --comment-sep CHAR     Comment separator [default:  ]
  --add-len              Add 'len=LENGTH' to the comments
  --add-initial-len      Add 'original_len=LENGTH' to the comments
  --add-gc               Add 'gc=%GC' to the comments
  --add-initial-gc       Add 'original_gc=%GC' to the comments
  --add-name             Add 'original_name=INITIAL_NAME' to the comments
  --add-ee               Add 'ee=EXPECTED_ERROR' to the comments
  --add-initial-ee       Add 'original_ee=EXPECTED_ERROR' to the comments

Filtering:
  -n, --max-ns INT       Discard sequences with more than INT Ns [default: -1]
  -m, --min-len INT      Discard sequences shorter than INT [default: 1]
  -x, --max-len INT      Discard sequences longer than INT, 0 to ignore [default: 0]
  --max-ee FLOAT         Discard sequences with higher than FLOAT expected error [default: -1.0]
  --trim-front INT       Trim INT base from the start of the sequence [default: 0]
  --trim-tail INT        Trim INT base from the end of the sequence [default: 0]
  --truncate INT         Keep only the first INT bases, 0 to ignore  [default: 0]
                         Negative values to print the last INT bases
  --max-bp INT           Stop printing each input file after INT bases [default: 0]

Output:
  -o, --output FILE      Write output to FILE (gzipped if ending in .gz) [default: -]
  --gz-level INT         Compression level for .gz output (0-9) [default: 6]
  --fasta                Force FASTA output
  --fastq                Force FASTQ output
  --report FILE          Save a report to FILE (original name, new name)
  --list                 Output a list of sequence names 
  --anvio                Output in Anvio format (-p c_ -s -z --zeropad 12 --report rename_report.txt)
  -q, --fastq-qual INT   Phred score assigned to bases when converting FASTA to FASTQ [default: 33]
  -v, --verbose          Verbose output
  --debug                Debug output
  -h, --help             Show this help

Input

One or more FASTA or FASTQ files. If no files are provided, the program will read from standard input. Additionally, you can add standard input to the list of input files. by adding -.

Output

It is possible to pass both FASTA and FASTQ inputs, but seqfu cat keeps a single output format instead of producing a mixed stream. By default the first printed record selects the output format. Use --fasta to normalize mixed inputs to FASTA, or --fastq when FASTA records should be emitted with a synthetic quality value. The -q/--fastq-qual option sets that quality as a Phred score (not an ASCII character or encoding offset). The default of 33 produces the character B in standard Phred+33 encoding, which corresponds to ~99.95% base-call accuracy. To assign a different quality, pass the desired Phred score directly, e.g. --fastq-qual 40 for I (Q40) or --fastq-qual 0 for ! (Q0). Using --list the simple list of records matching the criteria will be printed. When multiple input files are provided, --max-bp is applied separately to each input file.

Output goes to STDOUT unless -o FILE is given. If FILE ends in .gz the output is gzip-compressed (level set with --gz-level, default 6). This applies to --list/--long output too. seqfu cat refuses to write to a path that is also one of its inputs.

seqfu cat --min-len 100 -o filtered.fq.gz reads_R1.fq.gz

Anvi’o shortcut

If you use --anvio you will automatically suppress names and comments, and add a prefix c_ to the sequence names and leading zeros to the counter, and write the report to rename_report.txt. If you specify a different --report file, this will of course override the default report file.

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