Version 3.3.0

README.md

@@ -1,4 +1,4 @@
-<h1 align="center"><img width="300px" src="doc/img/isoseq3.png"/></h1>
+<h1 align="center"><img width="300px" src="doc/img/isoseq.png"/></h1>
 <h1 align="center">IsoSeq v3</h1>
 <p align="center">Scalable De Novo Isoform Discovery</p>
 
@@ -18,14 +18,15 @@ Latest version can be installed via bioconda package `isoseq3`.
 Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)
 for information on Installation, Support, License, Copyright, and Disclaimer.
 
-## Specific Version Documentation
+## Workflow Documentation
 
- * [Version 3.2, SMRT Link 8.0](README_v3.2.md)
- * [Version 3.1, SMRT Link 7.0](README_v3.1.md)
- * [Version 3.0, SMRT Link 6.0](README_v3.0.md)
+ * [Iso-Seq Clustering](isoseq-clustering.md)
+ * Iso-Seq Deduplication (UMIs and cell barcodes) [Future release]
 
 ## Changelog
- * **3.2.2**
+ * **3.3.0**
+   * SMRT Link release 9.0.0
+ * 3.2.2
    * Fix `polish` not generating fasta/q output. This bug was introduced in v3.2.0
  * 3.2.1
    * Fix a gff index 1-off bug in `collapse`
@@ -49,6 +50,12 @@ called `refine`. Your custom `primers.fasta` is used in this step to detect
 concatemers.
 
 ## FAQ
+### Where is the workflow starting from unpolished CCS reads?
+To simplify, unify, and future proof Iso-Seq, we decided to remove documentation
+starting from unpolished CCS reads. With the ever-increasing polymerase read
+lengths and improvements of CCS, going forward, it is recommended to generate
+polished CCS reads first and thus make final transcript polishing optional.
+
 ### Why IsoSeq v3 and not the established versions 1 or 2?
 The ever-increasing throughput of the Sequel system gave rise to the need for a
 scalable software solution that can handle millions of CCS reads, while
@@ -57,11 +64,11 @@ maintaining sensitivity and accuracy. Internal benchmarks have shown that
 [SQANTI](https://bitbucket.org/ConesaLab/sqanti) attributes *IsoSeq v3* a higher
 number of perfectly annotated isoforms:
 
-<img width="1000px" src="doc/img/isoseq3-performance.png"/>
+<img width="1000px" src="doc/img/isoseq-performance.png"/>
 
 Additional benefit, single linux binary that requires no dependencies.
 
-### Why is the number of transcripts much lower with IsoSeq3?
+### Why is the number of transcripts much lower with IsoSeq v3?
 Even though we also observe fewer polished transcripts with *IsoSeq v3*, the
 overall quality is much higher. Most of the low-quality transcripts are lost in the
 demultiplexing step. *Isoseq v1/2 classify* is too relaxed and is not filtering
@@ -70,18 +77,17 @@ effectively removes most molecules that are wrongly tagged, as in two 5' or two
 3' primers. Only a proper 5' and 3' primer pair allows to identify a full-length
 transcript and its orientation.
 
-
 ### I can't find the *classify* step
 Starting with version 3.1, *classify* functionality has been split into two tools.
 Removal of (barcoded) primers is performed with PacBio's standard demultiplexing
 tool *lima*. *Lima* does not remove poly(A) tails, nor detects concatemers.
-For this, `isoseq3 refine` generates FLNC reads.
+For this, `isoseq refine` generates FLNC reads.
 
 For version 3.0, poly(A) tail removal and concatemer detection is performed in
-`isoseq3 cluster`
+`isoseq cluster`
 
 ### My sample has poly(A) tails, how can I remove them?
-Use `--require-polya` for `isoseq3 refine`.
+Use `--require-polya` for `isoseq refine`.
 This filters for FL reads that have a poly(A) tail
 with at least 20 base pairs and removes identified tail.
 
@@ -107,7 +113,7 @@ feasible.
 *IsoSeq v3* deems two reads to stem from the same transcript, if they meet
 following criteria:
 
-<img width="1000px" src="doc/img/isoseq3-similar-transcripts.png"/>
+<img width="1000px" src="doc/img/isoseq-similar-transcripts.png"/>
 
 There is no upper limit on the number of gaps.
 
@@ -128,7 +134,7 @@ PacBio supports three different SMRTbell designs for IsoSeq libraries.
 In all designs, transcripts are labelled with asymmetric primers,
 whereas a poly(A) tail is optional. Barcodes may be optionally added.
 
-<img width="600px" src="doc/img/isoseq3-barcoding.png"/>
+<img width="600px" src="doc/img/isoseq-barcoding.png"/>
 
 ### The binary does not work on my linux system!
 Binaries require **SSE4.1 CPU support**; CPUs after 2008 (Penryn) include it.