seqfu cat

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 after INT bases [default: 0]

Output:
  --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   FASTQ default quality [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 mix FASTA and FASTQ files, and by default the program will produce a mixed output. Using --fasta or --fastq will force a specific output formats. For FASTA sequences a default quality values will be used. Using --list the simple list of records matching the criteria will be printed.

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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