Commit 3b67cb8f authored by Mathieu Giraud's avatar Mathieu Giraud

README.org: patient database, streamlined explanation on the Vidjil components

parent aec85525
......@@ -16,20 +16,24 @@ patient follow-up.
High-throughput sequencing (NGS/HTS) now enables the deep sequencing
of a lymphoid population with dedicated [[http://omictools.com/rep-seq-c424-p1.html][Rep-Seq]] methods and softwares.
Vidjil process high-througput sequencing data to *extract V(D)J
The Vidjil platform contains three components. The Vidjil algorithm
process high-througput sequencing data to *extract V(D)J
junctions and gather them into clones*. Vidjil starts
from a set of reads and detects "windows" overlapping the actual CDR3.
This is based on an fast and reliable seed-based heuristic and allows
to output the most abundant clones. Vidjil can also clusterize similar
clones, or leave this to the user after a manual review.
to output all sequenced clones. The analysis is extremely fast
because, in the first phase, no alignment is performed with database
germline sequences.
Vidjil also contains a *dynamic browser* for visualization and
The Vidjil *dynamic browser* is made for the visualization and
analysis of clones and their tracking along the time in a MRD setup or
in a immunological study. The browser can visualize data processed by
the algorithmic component of Vidjil or by other V(D)J analysis
pipelines.
the Vidjil algorithm or by other V(D)J analysis pipelines.
The browser enables to explore further cluterings proposed
by software and/or done manually done by the user.
Finally, a *server* is currently developed to link the browser and the
Finally, a *patient database* with a server
is currently developed to link the browser and the
algorithmic part. The goal is that the clinicians will be able to
upload, manage and process their runs directly on the browser (with
authentication).
......@@ -49,7 +53,7 @@ authentication).
- Development code is under [[browser/]]
- Documentation (in progress): [[doc/browser.org]]
** The server
** The server and the patient database
- Currently under development, code is in [[server/]]
- Planned first release: Q1 2015
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