merge of origin/main

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)
+========================

docs/index.rst

@@ -13,4 +13,5 @@ Contents:
    :maxdepth: 1
 
    about
-   1- Library_preparation_key_concepts
+   1- Library_preparation
+   2- Sequencing_technologies