[med-svn] [pbdagcon] 04/08: Add a manpage for pbdagcon based on README file

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository pbdagcon.

commit 573937df7b3edaae3e45c49e486113ed8d939acc
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Dec 11 00:14:45 2015 -0800

    Add a manpage for pbdagcon based on README file
---
 debian/manpages   |  1 +
 debian/pbdagcon.1 | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..058363a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/pbdagcon.1
diff --git a/debian/pbdagcon.1 b/debian/pbdagcon.1
new file mode 100644
index 0000000..292cef3
--- /dev/null
+++ b/debian/pbdagcon.1
@@ -0,0 +1,32 @@
+.TH PBDAGCON 1 "December 2015"
+.SH NAME
+pbdagcon \- sequence consensus using directed acyclic graphs
+.SH DESCRIPTION
+.B pbdagcon
+is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.
+
+It uses the alignment information from
+.BR blasr (1)
+to align sequence reads to a "backbone" sequence.
+Based on the underlying alignment directed acyclic graph (DAG), it will be able to use the new information from the reads to find the discrepancies between the reads and the "backbone" sequences.
+A dynamic programming process is then applied to the DAG to find the optimum sequence of bases as the consensus.
+The new consensus can be used as a new backbone sequence to iteratively improve the consensus quality.
+
+While the code is developed for processing PacBio(TM) raw sequence data, the algorithm can be used for general consensus purpose.
+Currently, it only takes FASTA input.
+For shorter read sequences, one might need to adjust the
+.BR blasr (1)
+alignment parameters to get the alignment string properly.
+
+The code and the underlying graphical data structure have been used for some algorithm development prototyping including phasing reads, pre-assembly and a work around to generate consensus from intermediate Celera Assembler outputs.
+
+.SH OPTIONS
+A summary of options is available from the program's help menu.
+.TP
+.B \-\-help
+Show summary of options.
+
+.SH SEE ALSO
+.BR blasr (1),
+.br
+/usr/share/doc/pbdagcon/examples

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbdagcon.git