seqfu rc

rc is one of the core subprograms of SeqFu, that allows to print the reverse complement of sequences, either from input files or provided as strings. IUPAC DNA characters allowed.

Usage: rc [options] [<strings-or-files>...] 

Print the reverse complementary of sequences in files or sequences
given as parameters

Options:
  -s, --seq-name NAME    Sequence name if coming as string [default: string]
  --strip-comments       Remove sequence comments
  -v, --verbose          Verbose output
  --help                 Show this help

Reverse complement strings

To print the reverse complement of sequence, for example of universal primers with degenerate bases:

seqfu rc CCTACGGGNGGCWGCAG GGACTACHVGGGTATCTAATCC

will produce:

>string_1
CTGCWGCCNCCCGTAGG
>string_2
GGATTAGATACCCBDGTAGTCC

Note: if a single sequence (string) is provided, the output is not in FASTA format but a plain string. This makes easier a programmatic use like:

removePrimersScript.sh --for $FOR --rev $(seqfu rc $REV)

Reverse commplement files

When supplying input files, the whole file will be complemented. If the file is in FASTQ format the quality will be reversed as well. The program can process multiple files.

seqfu rc data/test.fasta

will produce:

>SEQ1_BamHI-EcoRI
ACGTGTACCAGCTACGATCGTGTGTAGCTAGCTCGTCAGCTAGCTACGTCGATCACGTACGCTGT
>Seq2 with comm
GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
>Seq3
GGGGGGGGGGGGGGGGGGGGG