1 and 2 rst information added

docs/1- Library_preparation.rst

@@ -12,7 +12,7 @@ Depending on the sample nature and the nucleic acid (RNA or DNA) the extraction
 Thus, a rigorous quality control of the nucleic acid quantification extraction must to be performed, to asses the **quantity, purity and integrity**. DNA Typically could be measured whether
 UV spectrocopy (Nanodrop) or electrophoresis (Agilent TapeStation), RNA concentration is typically measured by Qubit fluorometer (ThermoFisherScientific).
 
-.. note::
+.. danger::
 	**RNA is more critical**, sample contamination is very common. 
 
 
@@ -25,6 +25,7 @@ In a nutshell, library is defined as a collection of nucleic acid (RNA or DNA) f
 .. image:: images/library_prep_explanation_Van_Djik_2014.jpg
   :width: 400
 
+*source: https://doi.org/10.1016/j.yexcr.2014.01.008*
 
 Main steps of a Library Preparation Kit:
 
@@ -58,10 +59,21 @@ removal of unwanted products to leave only the nucleic acid fragments. Often is
 
 Check if DNA mmets the quantity and quality requirements od the sequencing instrument. Assesss the quantity and size distribution of the library. 
 
-
-RNA Library preparation 
+Library preparation bias 
 ========================
 
+..tabs::
+
+	..group-tab:: DNA library bias
+
+	  DNA Library preparation bias 
+	  ----------------------------
+
+	..group-tab:: RNA library bias
+
+	  RNA Library preparation bias 
+	  ----------------------------
+
 Due that RNA is converted to cDNA, PCR-amplified libraries are necessary for many sequencing instruments.
 
 RNA-seq applications requires the removal of the ribosomal RNA (rRNA), comprising up to 90% of the total RNA. rRNA can be isolated and removed by hybridisation
@@ -70,5 +82,7 @@ capture using rRNA-specific probes, then isolated from RNA sample using magnetic
 For especific isolation of mRNA transcripts, in addition to rRNA depletion, poly(A) must be done for selecting the RNAs containing a polyadenilated tail using oligo primers.
 
 
-Library preparation factors to consider
-========================
+
+
+
+

docs/2- Sequencing_technologies.rst

@@ -1,6 +1,62 @@
 .. _Library_preparation-page:
 
-*******************
+******************************
 2 Main Sequencing Technologies
-*******************
+******************************
 
+Short Reads sequencing (Illumina)
+=================================
+
+It consist in The  polymerase-mediated Sequencing by synthesis (SBS), this works by coupling the four DNA bases to fluorescent markers alongside a terminator chemical group that pauses DNA synthesis.
+While DNA is being synthesized, each fluorescent marker is optically verified before the tag and terminator are removed, and the next step in the sequence is recorded. 
+
+#. Cluster generation
+
+Adapter attached to the DNA fragment is used to hybridisation to the flowcell, subsequentlty PCR amplification (bridge amplification) generates a cluster of the same sequence fragment to amplify the signal
+when the nucleotide base is synthesized, thus obtaining a multiple cluster on a Flow Cell. 
+
+.. image:: images/illumina_Lu_et_al_2016.png
+  :width: 400
+
+*Source: https://www.researchgate.net/publication/357946568_New_approaches_and_concepts_to_study_complex_microbial_communities*
+
+
+#. Sequencing
+
+On each cycle is incorporated one nucleotide to the template, it correspond to the read length (1'' cycles equal to 100 bp read length). 
+After imaging to determine which of the four colours was incorporated in each cluster of the flow cell. 
+
+Single end 
+----------
+
+Correspond to the basis of SBS, where the nucleotides added to the template sequence is read from one end of the fragment. 
+It's more simple and effcient, due to reduce the the number of stemps in the library preparation.
+
+nevertheless, the quality of nucleotides decreases as the sequencing process progresses.
+
+
+Paired end
+----------
+
+*source: https://systemsbiology.columbia.edu/genome-sequencing-defining-your-experiment#:~:text=Single%2Dend%20vs.&text=In%20single%2Dend%20reading%2C%20the,opposite%20end%20of%20the%20fragment.*
+
+During library preparation  are incorporated sequencing primers binding site at both ends of the DNA fragments. 
+This allows to reading at one read, when it finiches this direction at the specified read lenght, then starts another round od reading from the opposite end of the fragemnt. 
+It improves:
+
+- The confidence of the sequence read
+- The ability to identify the relative positions of various reads in the genome (much more efficient in resolve rearrangements such as insertions, deletions or inversions)
+- Can improve the assembly of repetitive regions. 
+- On the ohter hand is more expensive and time-consuming (respect single end)
+
+
+.. seealso::
+	.. _Illumina_sequencing_by_synthesis_workflow: https://www.youtube.com/watch?v=fCd6B5HRaZ8
+
+	   See the _Illumina_sequencing_by_synthesis_workflow video by Illumina to visualize the concepts of SBS. 
+
+
+For more information 
+
+Long read sequencing (Nanopore)
+========================