Commit b5116970 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/: both Rep-Seq and AIRR-Seq are used now

and omictools.com does not exist anymore
parent 75fda2d1
......@@ -9,8 +9,8 @@ pathologies, and in leukemia, are used to quantify the minimal residual
disease during patient follow-up.
With adapted [library preparation and sequencing](locus.md),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
### Life scientist
- Tutorial "Mastering the Vidjil web application":
......
......@@ -2,9 +2,9 @@
[V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are essential for immunological diversity.
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
High-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
# Library preparation and sequencing for human RepSeq studies
......
......@@ -5,8 +5,8 @@ Vidjil is an open-source platform for the analysis of high-throughput sequencing
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
This is the help of the [Vidjil web application](http://app.vidjil.org/).
Further help can always be asked to <support@vidjil.org>. We can also arrange phone or video meeting.
......@@ -420,7 +420,7 @@ inside a clone can have different lengths or can be shifted,
especially in the case of overlapping paired-end sequencing. There can be also
some sequencing errors.
The `.vidjil` file has to give one consensus sequence per clone, and
Rep-Seq algorithms have to deal with great care to these difference in
RepSeq algorithms have to deal with great care to these difference in
order not to gather reads from different clones.
For **vidjil-algo**, it is required that the window centered on
......
......@@ -28,8 +28,8 @@ leukemia, are used to quantify the minimal residual disease during
patient follow-up.
With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
Vidjil-algo processes high-throughput sequencing data to extract V(D)J
junctions and gather them into clones. Vidjil-algo starts
......
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