Rename IsoSeq3 to IsoSeq v3

README.md

@@ -1,16 +1,16 @@
 <h1 align="center"><img width="300px" src="doc/img/isoseq3.png"/></h1>
-<h1 align="center">IsoSeq3</h1>
+<h1 align="center">IsoSeq v3</h1>
 <p align="center">Scalable De Novo Isoform Discovery</p>
 
 ***
 
-*IsoSeq3* contains the newest tools to identify transcripts in
+*IsoSeq v3* contains the newest tools to identify transcripts in
 PacBio single-molecule sequencing data.
 Starting in SMRT Link v6.0.0, those tools power the
-*IsoSeq3 GUI-based analysis* application.
+*IsoSeq GUI-based analysis* application.
 A composable workflow of existing tools and algorithms, combined with
 a new clustering technique, allows to process the ever-increasing yield of PacBio
-machines with similar performance to *IsoSeq1* and *IsoSeq2*.
+machines with similar performance to *IsoSeq* versions 1 and 2.
 
 ## Availability
 Latest version can be installed via bioconda package `isoseq3`.
@@ -46,22 +46,22 @@ called `refine`. Your custom `primers.fasta` is used in this step to detect
 concatemers.
 
 ## FAQ
-### Why IsoSeq3 and not the established IsoSeq1 or IsoSeq2?
+### 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
 maintaining sensitivity and accuracy. Internal benchmarks have shown that
-*IsoSeq3* is orders of magnitude faster than currently employed solutions and
-[SQANTI](https://bitbucket.org/ConesaLab/sqanti) attributes *IsoSeq3* a higher
+*IsoSeq v3* is orders of magnitude faster than currently employed solutions and
+[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"/>
 
 Additional benefit, single linux binary that requires no dependencies.
 
 ### Why is the number of transcripts much lower with IsoSeq3?
-Even though we also observe fewer polished transcripts with *IsoSeq3*, the
+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. *Isoseq1/2 classify* is too relaxed and is not filtering
+demultiplexing step. *Isoseq v1/2 classify* is too relaxed and is not filtering
 junk molecules to a satisfactory level. In fact, *lima* calls are spot on and
 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
@@ -89,7 +89,7 @@ whole transcriptome sample can finish clustering in minutes, whereas a single
 gene amplification of 10kb transcripts can take a couple of hours.
 
 ### Which clustering algorithm is used?
-In contrast to its predecessors, *IsoSeq3* does not rely on NP-hard clique
+In contrast to its predecessors, *IsoSeq v3* does not rely on NP-hard clique
 finding, but uses a hierarchical alignment strategy with `O(N*log(N))`.
 Recent advances in rapid alignment of long reads make this this approach
 feasible.
@@ -101,7 +101,7 @@ feasible.
 *Polish* uses up to 60 subreads to polish the cluster consensus.
 
 ### When are two reads clustered?
-*IsoSeq3* deems two reads to stem from the same transcript, if they meet
+*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"/>

README_v3.0.md

@@ -1,16 +1,16 @@
 <h1 align="center"><img width="300px" src="doc/img/isoseq3.png"/></h1>
-<h1 align="center">IsoSeq 3.0</h1>
+<h1 align="center">IsoSeq v3.0</h1>
 <p align="center">Scalable De Novo Isoform Discovery</p>
 
 ***
 
-*IsoSeq3* contains the newest tools to identify transcripts in
+*IsoSeq v3.0* contains the newest tools to identify transcripts in
 PacBio single-molecule sequencing data.
 Starting in SMRT Link v6.0.0, those tools power the
-*IsoSeq3 GUI-based analysis* application.
+*IsoSeq GUI-based analysis* application.
 A composable workflow of existing tools and algorithms, combined with
 a new clustering technique, allows to process the ever-increasing yield of PacBio
-machines with similar performance to *IsoSeq1* and *IsoSeq2*.
+machines with similar performance to *IsoSeq* versions 1 and 2.
 
 ## Availability
 Latest version can be installed via bioconda package `isoseq3`.
@@ -76,7 +76,7 @@ The following are examples for barcoded samples using a 16bp barcode followed by
 From here on, execute the following steps for each output BAM file.
 
 ### Clustering and polishing
-*IsoSeq3* wraps all tools into one fat binary.
+*IsoSeq v3* wraps all tools into one fat binary.
 
     $ isoseq3
     isoseq3 - De Novo Transcript Reconstruction
@@ -92,7 +92,7 @@ From here on, execute the following steps for each output BAM file.
         isoseq3 summarize polished.bam summary.csv
 
 #### Clustering and transcript clean up
-Compared to previous IsoSeq approaches, *IsoSeq3* performs a single clustering
+Compared to previous IsoSeq approaches, *IsoSeq v3* performs a single clustering
 technique.
 Due to the nature of the algorithm, it can't be efficiently parallelized. It is advised to give this step as many cores
 as possible. The individual steps of *cluster* are as following:

README_v3.1.md

@@ -1,16 +1,16 @@
 <h1 align="center"><img width="300px" src="doc/img/isoseq3.png"/></h1>
-<h1 align="center">IsoSeq 3.1</h1>
+<h1 align="center">IsoSeq v3.1</h1>
 <p align="center">Scalable De Novo Isoform Discovery</p>
 
 ***
 
-*IsoSeq3* contains the newest tools to identify transcripts in
+*IsoSeq v3.1* contains the newest tools to identify transcripts in
 PacBio single-molecule sequencing data.
-Starting in SMRT Link v6.0.0, those tools power the
-*IsoSeq3 GUI-based analysis* application.
+Starting in SMRT Link v7.0.0, those tools power the
+*IsoSeq GUI-based analysis* application.
 A composable workflow of existing tools and algorithms, combined with
 a new clustering technique, allows to process the ever-increasing yield of PacBio
-machines with similar performance to *IsoSeq1* and *IsoSeq2*.
+machines with similar performance to *IsoSeq* versions 1 and 2.
 
 ## Availability
 Latest version can be installed via bioconda package `isoseq3`.
@@ -151,7 +151,7 @@ Similarly, merge all of your **source** `<movie>.subreadset.xml` files:
     $ dataset create --type SubreadSet merged.subreadset.xml movie1.subreadset.xml movie2.subreadset.xml movieN.subreadset.xml
 
 ### Step 4 - Clustering
-Compared to previous IsoSeq approaches, *IsoSeq3* performs a single clustering
+Compared to previous IsoSeq approaches, *IsoSeq v3* performs a single clustering
 technique.
 Due to the nature of the algorithm, it can't be efficiently parallelized.
 It is advised to give this step as many coresas possible.

README_v3.2.md

@@ -1,19 +1,19 @@
 <h1 align="center"><img width="300px" src="doc/img/isoseq3.png"/></h1>
-<h1 align="center">IsoSeq 3.2</h1>
+<h1 align="center">IsoSeq v3.2</h1>
 <p align="center">Scalable De Novo Isoform Discovery</p>
 
 ***
 
-*IsoSeq3* contains the newest tools to identify transcripts in
+*IsoSeq v3.2* contains the newest tools to identify transcripts in
 PacBio single-molecule sequencing data.
-Starting in SMRT Link v6.0.0, those tools power the
-*IsoSeq3 GUI-based analysis* application.
+Starting in SMRT Link v8.0.0, those tools power the
+*IsoSeq GUI-based analysis* application.
 A composable workflow of existing tools and algorithms, combined with
 a new clustering technique, allows to process the ever-increasing yield of PacBio
-machines with similar performance to *IsoSeq1* and *IsoSeq2*.
+machines with similar performance to *IsoSeq* versions 1 and 2.
 
 Focus of version 3.2 documentation is processing of polished CCS reads,
-the latest feature of *IsoSeq3*. Processing of unpolished CCS reads with final
+the latest feature of *IsoSeq v3*. Processing of unpolished CCS reads with final
 transcript polishing is still supported, please refer to the
 [documentation of version 3.1](README_v3.1.md).
 
@@ -145,7 +145,7 @@ Merge all of your `<movie>.flnc.bam` files:
     $ dataset create --type TranscriptSet merged.flnc.xml movie1.flnc.bam movie2.flnc.bam movieN.flnc.bam
 
 ### Step 4 - Clustering
-Compared to previous IsoSeq approaches, *IsoSeq3* performs a single clustering
+Compared to previous IsoSeq approaches, *IsoSeq v3* performs a single clustering
 technique.
 Due to the nature of the algorithm, it can't be efficiently parallelized.
 It is advised to give this step as many coresas possible.