🚨 SQANTI3 release alert!! 🚨 v5.3.0 is now LIVE!!! The new release includes better file compatibility, improved parallelization, a wrapper to run QC-filter-resque, and the first release of our newest tool, 👀 SQANTI-reads 🎉!
Thanks a lot to the whole team!
github.com/ConesaLab/SQ...
Thanks a lot to the whole team!
github.com/ConesaLab/SQ...
Release SQANTI 5.3.0 · ConesaLab/SQANTI3
This release include some new minor features, such as the inclusion of a Dockerfile of sqanti and a wrapper to execute all SQANTI steps at once. Also enhances compatibility for fastq.gz files in sq...
github.com
December 4, 2024 at 9:17 AM
🚨 SQANTI3 release alert!! 🚨 v5.3.0 is now LIVE!!! The new release includes better file compatibility, improved parallelization, a wrapper to run QC-filter-resque, and the first release of our newest tool, 👀 SQANTI-reads 🎉!
Thanks a lot to the whole team!
github.com/ConesaLab/SQ...
Thanks a lot to the whole team!
github.com/ConesaLab/SQ...
Not 1, not 2, but 3 new papers by @conesalab.bsky.social published today in the special issue on long-read sequencing. Find our latest work on SQANTI-reads, genome annotation with lrRNA-seq evidence, and a Perspective in Transcript Divergence. tinyurl.com/GRLong @longtrec.bsky.social
Long-read Sequencing Special Collection
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
tinyurl.com
April 15, 2025 at 3:20 PM
Not 1, not 2, but 3 new papers by @conesalab.bsky.social published today in the special issue on long-read sequencing. Find our latest work on SQANTI-reads, genome annotation with lrRNA-seq evidence, and a Perspective in Transcript Divergence. tinyurl.com/GRLong @longtrec.bsky.social
New @pacbio.bsky.social #bioinformatics spotlight video is up! SQANTI-QC: a multi-sample long-read RNA-Seq QC tool! Demo included. Check it out and give it a try! www.youtube.com/watch?v=83XL...
Using SQANTI-reads for long-read RNA-Seq quality control
YouTube video by PacBio
www.youtube.com
November 5, 2025 at 9:33 PM
New @pacbio.bsky.social #bioinformatics spotlight video is up! SQANTI-QC: a multi-sample long-read RNA-Seq QC tool! Demo included. Check it out and give it a try! www.youtube.com/watch?v=83XL...
@longtrec.bsky.social is presenting the latest & hottest long-read transcriptomics research at #ISMBECCB2025! Posters D-176 (isONclust3), C-207 (Multisample isoforms), C-237 (TSS prediction), D-202 (Single-cellSQANTI), and talks at iRNA (TUSCO, Amanita) and HitSeq (SQANTI-reads) @hitseq.bsky.social
July 21, 2025 at 10:28 AM
@longtrec.bsky.social is presenting the latest & hottest long-read transcriptomics research at #ISMBECCB2025! Posters D-176 (isONclust3), C-207 (Multisample isoforms), C-237 (TSS prediction), D-202 (Single-cellSQANTI), and talks at iRNA (TUSCO, Amanita) and HitSeq (SQANTI-reads) @hitseq.bsky.social
What we build: SQANTI3, SQANTI-SIM, SQANTI-reads and TUSCO for long-read QC and benchmarking; tappAS and IsoAnnot for isoform-level function; acorde and scMaSigPro for single cell; maSigPro, NOISeq, PaintOmics, MultiBaC and MOSim for multi-omics. All open source.
August 30, 2026 at 3:41 PM
What we build: SQANTI3, SQANTI-SIM, SQANTI-reads and TUSCO for long-read QC and benchmarking; tappAS and IsoAnnot for isoform-level function; acorde and scMaSigPro for single cell; maSigPro, NOISeq, PaintOmics, MultiBaC and MOSim for multi-omics. All open source.
SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser https://www.biorxiv.org/content/10.64898/2026.05.25.727625v1
May 28, 2026 at 4:47 PM
SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser https://www.biorxiv.org/content/10.64898/2026.05.25.727625v1
Excited to share the latest preprint from @conesalab.bsky.social. A new tool to visualize and filter isoforms based on SQANTI things within the UCSC Genome Browser. Awesome work led by @carolinamonzo.bsky.social and with collaboration from @ucscgenomics.bsky.social
tinyurl.com/SQANTI-br #longreads
tinyurl.com/SQANTI-br #longreads
May 29, 2026 at 11:14 AM
Excited to share the latest preprint from @conesalab.bsky.social. A new tool to visualize and filter isoforms based on SQANTI things within the UCSC Genome Browser. Awesome work led by @carolinamonzo.bsky.social and with collaboration from @ucscgenomics.bsky.social
tinyurl.com/SQANTI-br #longreads
tinyurl.com/SQANTI-br #longreads
Isoform classification - a largely solved #bioinformatics problem. (hot take? come at me 🌶️)
One of the most popular isoform classification tool is SQANTI. Now in its 3rd version (SQANTI3) it is also implemented as `pigeon` in @pacbio.bsky.social SMRT Link software www.biorxiv.org/content/10.1...
One of the most popular isoform classification tool is SQANTI. Now in its 3rd version (SQANTI3) it is also implemented as `pigeon` in @pacbio.bsky.social SMRT Link software www.biorxiv.org/content/10.1...
SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
February 16, 2024 at 9:42 PM
Isoform classification - a largely solved #bioinformatics problem. (hot take? come at me 🌶️)
One of the most popular isoform classification tool is SQANTI. Now in its 3rd version (SQANTI3) it is also implemented as `pigeon` in @pacbio.bsky.social SMRT Link software www.biorxiv.org/content/10.1...
One of the most popular isoform classification tool is SQANTI. Now in its 3rd version (SQANTI3) it is also implemented as `pigeon` in @pacbio.bsky.social SMRT Link software www.biorxiv.org/content/10.1...
And to close, the one who made it all possible. 🌅
Closing keynote: Prof. Ana Conesa on SQANTIverse, a unifying framework for long-read transcriptomics.
LongTREC coordinator, VALT organiser, and a field-shaper for years. No one better to end on.
Thank you, Ana. 💙
#VALT2026 #LongReads #SQANTI
Closing keynote: Prof. Ana Conesa on SQANTIverse, a unifying framework for long-read transcriptomics.
LongTREC coordinator, VALT organiser, and a field-shaper for years. No one better to end on.
Thank you, Ana. 💙
#VALT2026 #LongReads #SQANTI
July 1, 2026 at 3:04 PM
And to close, the one who made it all possible. 🌅
Closing keynote: Prof. Ana Conesa on SQANTIverse, a unifying framework for long-read transcriptomics.
LongTREC coordinator, VALT organiser, and a field-shaper for years. No one better to end on.
Thank you, Ana. 💙
#VALT2026 #LongReads #SQANTI
Closing keynote: Prof. Ana Conesa on SQANTIverse, a unifying framework for long-read transcriptomics.
LongTREC coordinator, VALT organiser, and a field-shaper for years. No one better to end on.
Thank you, Ana. 💙
#VALT2026 #LongReads #SQANTI
🚀 SQANTI-verse Cards are here! ✨
If you want to get'em all, just follow these steps:
1️⃣ Use one of the SQANTI tools from our Github
2️⃣ Generate amazing data and publish your results
3️⃣ Tag us when you share your publication
We’ll send you a card!
8 are already available & more are coming 🌌
#SQANTIverse
If you want to get'em all, just follow these steps:
1️⃣ Use one of the SQANTI tools from our Github
2️⃣ Generate amazing data and publish your results
3️⃣ Tag us when you share your publication
We’ll send you a card!
8 are already available & more are coming 🌌
#SQANTIverse
June 3, 2025 at 9:50 AM
🚀 SQANTI-verse Cards are here! ✨
If you want to get'em all, just follow these steps:
1️⃣ Use one of the SQANTI tools from our Github
2️⃣ Generate amazing data and publish your results
3️⃣ Tag us when you share your publication
We’ll send you a card!
8 are already available & more are coming 🌌
#SQANTIverse
If you want to get'em all, just follow these steps:
1️⃣ Use one of the SQANTI tools from our Github
2️⃣ Generate amazing data and publish your results
3️⃣ Tag us when you share your publication
We’ll send you a card!
8 are already available & more are coming 🌌
#SQANTIverse
That said, SQANTI has been a huge help in trying to sift through that and figure it out
February 18, 2024 at 8:27 PM
That said, SQANTI has been a huge help in trying to sift through that and figure it out
The @bcbhubcsic.bsky.social from @csic.es sponsors #ISMBECCB2025 with travel fellowships. Check out the posters by the young researchers of our network: D-202 (Carlos Blanco: SQANTI-single cell); C-536 (Yosra Berrouayel: TFEA.ChIP), D-495 (Alicia Santamaria: Chromatinsight).
July 22, 2025 at 11:22 AM
The @bcbhubcsic.bsky.social from @csic.es sponsors #ISMBECCB2025 with travel fellowships. Check out the posters by the young researchers of our network: D-202 (Carlos Blanco: SQANTI-single cell); C-536 (Yosra Berrouayel: TFEA.ChIP), D-495 (Alicia Santamaria: Chromatinsight).
Hello everybody!
Great news from the lab, as Julen Santiago, one of our PhD Candidates, has done an amazing contribution to the SQANTI-verse. He has fixed tappAS! 🤩
Go to tappAS GitHub to download its latest relase and have fun!
github.com/ConesaLab/ta...
Great news from the lab, as Julen Santiago, one of our PhD Candidates, has done an amazing contribution to the SQANTI-verse. He has fixed tappAS! 🤩
Go to tappAS GitHub to download its latest relase and have fun!
github.com/ConesaLab/ta...
GitHub - ConesaLab/tappAS: This repository contains the source code for the tappAS application. See README for details.
This repository contains the source code for the tappAS application. See README for details. - ConesaLab/tappAS
github.com
July 31, 2025 at 10:33 AM
Hello everybody!
Great news from the lab, as Julen Santiago, one of our PhD Candidates, has done an amazing contribution to the SQANTI-verse. He has fixed tappAS! 🤩
Go to tappAS GitHub to download its latest relase and have fun!
github.com/ConesaLab/ta...
Great news from the lab, as Julen Santiago, one of our PhD Candidates, has done an amazing contribution to the SQANTI-verse. He has fixed tappAS! 🤩
Go to tappAS GitHub to download its latest relase and have fun!
github.com/ConesaLab/ta...
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. https://www.biorxiv.org/content/10.1101/2024.08.23.609463v1
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. https://www.biorxiv.org/content/10.1101/2024.08.23.609463v1
SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to deve
www.biorxiv.org
August 26, 2024 at 3:47 AM
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. https://www.biorxiv.org/content/10.1101/2024.08.23.609463v1
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark https://www.biorxiv.org/content/10.1101/2023.08.23.554392v1
August 25, 2023 at 4:56 PM
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark https://www.biorxiv.org/content/10.1101/2023.08.23.554392v1
Tim - that’s an interesting case! AFAIK Graph genomes are still not prevalent and the biggest issue would be matching annotations that understand graph genomes. SQANTI ultimately relies on the genome and annotation to match. But they exist I don’t see why it can’t be done .
February 19, 2024 at 5:08 PM
Tim - that’s an interesting case! AFAIK Graph genomes are still not prevalent and the biggest issue would be matching annotations that understand graph genomes. SQANTI ultimately relies on the genome and annotation to match. But they exist I don’t see why it can’t be done .
2/ The concept of SQANTI(3)/pigeon is simple - classify a full-length transcript isoform based on its splicing pattern - exons, junctions, start/end - against a reference annotation like GENCODE and largely categorize it as "known" or "novel".
February 16, 2024 at 9:44 PM
2/ The concept of SQANTI(3)/pigeon is simple - classify a full-length transcript isoform based on its splicing pattern - exons, junctions, start/end - against a reference annotation like GENCODE and largely categorize it as "known" or "novel".
Quality assessment of long read data in multisample lrRNA-seq experiments with SQANTI-reads
#Drosophila
#Drosophila
Quality assessment of long read data in multisample lrRNA-seq experiments with SQANTI-reads
#Drosophila
PubMed link
pubmed.ncbi.nlm.nih.gov
March 4, 2025 at 5:23 AM
Quality assessment of long read data in multisample lrRNA-seq experiments with SQANTI-reads
#Drosophila
#Drosophila
Cool idea of universal single-isoform genes (BUGSI) to assess RNA data as part of SQANTI ecosystem. Great talk by Ana Conesa at #biodata24
SQANTI-Sim: link.springer.com/article/10.1186/s13059-023-03127-0 SQANTI3 for quality control long-read transcriptomes github.com/ConesaLab/SQANTI3 #cshldata24
SQANTI-Sim: link.springer.com/article/10.1186/s13059-023-03127-0 SQANTI3 for quality control long-read transcriptomes github.com/ConesaLab/SQANTI3 #cshldata24
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark - Genome Biology
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and no...
link.springer.com
November 14, 2024 at 4:03 AM
Cool idea of universal single-isoform genes (BUGSI) to assess RNA data as part of SQANTI ecosystem. Great talk by Ana Conesa at #biodata24
SQANTI-Sim: link.springer.com/article/10.1186/s13059-023-03127-0 SQANTI3 for quality control long-read transcriptomes github.com/ConesaLab/SQANTI3 #cshldata24
SQANTI-Sim: link.springer.com/article/10.1186/s13059-023-03127-0 SQANTI3 for quality control long-read transcriptomes github.com/ConesaLab/SQANTI3 #cshldata24
SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser https://www.biorxiv.org/content/10.64898/2026.05.25.727625v1
May 28, 2026 at 4:47 PM
SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser https://www.biorxiv.org/content/10.64898/2026.05.25.727625v1
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. https://www.biorxiv.org/content/10.1101/2024.08.23.609463v1
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. https://www.biorxiv.org/content/10.1101/2024.08.23.609463v1
SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to deve
www.biorxiv.org
August 26, 2024 at 3:47 AM
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. https://www.biorxiv.org/content/10.1101/2024.08.23.609463v1
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark https://www.biorxiv.org/content/10.1101/2023.08.23.554392v1
August 25, 2023 at 4:56 PM
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark https://www.biorxiv.org/content/10.1101/2023.08.23.554392v1
Long reads, full throttle. 🧬
This afternoon's workshop belongs to Pacific Biosciences, with Kinnex front and centre: large-scale automatable RNA-seq, full-length isoform workflows, and SQANTI tooling stretching from bulk to single-cell and single-nuclei.
#VALT2026 #LongReads #Kinnex #IsoSeq
This afternoon's workshop belongs to Pacific Biosciences, with Kinnex front and centre: large-scale automatable RNA-seq, full-length isoform workflows, and SQANTI tooling stretching from bulk to single-cell and single-nuclei.
#VALT2026 #LongReads #Kinnex #IsoSeq
June 30, 2026 at 12:18 PM
Long reads, full throttle. 🧬
This afternoon's workshop belongs to Pacific Biosciences, with Kinnex front and centre: large-scale automatable RNA-seq, full-length isoform workflows, and SQANTI tooling stretching from bulk to single-cell and single-nuclei.
#VALT2026 #LongReads #Kinnex #IsoSeq
This afternoon's workshop belongs to Pacific Biosciences, with Kinnex front and centre: large-scale automatable RNA-seq, full-length isoform workflows, and SQANTI tooling stretching from bulk to single-cell and single-nuclei.
#VALT2026 #LongReads #Kinnex #IsoSeq
Continuing the epigenome theme at #VALT2026: Tianyuan Liu on SQANTI-Epi, integrating Fiber-seq with long-read RNA-seq to link chromatin state to isoform regulation.
#LongTREC #VALT2026 #lrRNAseq #transcriptomics
#LongTREC #VALT2026 #lrRNAseq #transcriptomics
June 29, 2026 at 8:07 AM
Continuing the epigenome theme at #VALT2026: Tianyuan Liu on SQANTI-Epi, integrating Fiber-seq with long-read RNA-seq to link chromatin state to isoform regulation.
#LongTREC #VALT2026 #lrRNAseq #transcriptomics
#LongTREC #VALT2026 #lrRNAseq #transcriptomics