Biomedical Engineering Reference
In-Depth Information
3 Move or copy the
phredPhrap
script into the
edit_dir
subdirectory.
4Runthe
phredPhrap
script, which automates several steps:
(a)
Phred
for basecalling and conversion of reads to PHD format
(b)
Phd2fasta
, to convert the PHD files from
Phred
to FASTA format
(c)
Cross_match
, to mask vector sequence
(d)
Phrap
, to assemble the reads and build an ACE file
t
(e) Additional ancillary programs to aid visualization in
Consed
.
Notes
r
Available from http://www.phrap.org. [20].
s
Available from http://droog.gs.washington.edu/polyphred [19].
t
Typically, assemblies are written to ACE (.ace) files, a format utilized by many downstream
analysis tools.
Figure 2.1
SNP detection in ABI 3730 sequence data with NovoSNP. SNP discovery efforts can
be organized by projects, each with its own reference sequence (top left). Raw sequence files
are basecalled and aligned to the reference sequence, after which a list of candidate sequence
changes (left) is generated. Each prediction can be manually reviewed by visualizing the traces
as they align to the reference sequence (right). (See Plate 2.1.)
