Read ACE format assembly files

These are typically output by sequence assembly tools, like CAP3 or Phrap.

Documented in the section labelled "ACE FILE FORMAT" at http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt

Briefly: each field is a line starting with a two letter code, in some cases followed by data lines termintated by a blank line. Here's an brief example how an ACE file looks like:

         AS contigs reads
         CO contig_name bases reads segments compl (CAP3: segments=0)
         sequence
         BQ base_qualities
         AF read1 compl padded_start_consensus (negatives meaning?)
         AF read2 ..
         BS segments
         RD read1 bases info_items info_tags (latter two set to 0 by CAP3)
         sequence
         QA read1 qual_start qual_end align_start align_end
         DS (phred header? left empty by CAP3)
         RD read2 ...
  

As far as I know, this is only used for nucleotide sequences.