long-read-tools

Twitter account maintained by Aims to provide easy access to available long read sequence data analysis tools.

[long-read-tools @long_read_tools]

We sailed over 1k tools with the latest update 🚀! Thanks for your submissions.
With that, we’ll move to BlueSky @long-read-tools.bsky.social
See you there!
https://t.co/Uj7OEnbnZA

[Martin Smith @martinalexsmith]

Apparently a new @PacBio machine just announced at #ASHG24, Vega: A bench top HiFi system:
- 60 Gbases per 12-24h video
- Same quality as Revio

[long-read-tools @long_read_tools]

25 tools and 2 benchmarks added to https://t.co/AwtorFuWw0.
Next update will take us over 1k tools!

[Matthew Parker @bioinfomatt]

Absolutely mega release from the @nanopore EPI2ME team including big speed ups for wf-human-variation, a new BAC mode for wf-clone- validation, tumour only more for wf-somatic-variation and many many more improvements and bug fixes!

https://t.co/OIeCbY3J3c

#AGBT #AGBT24

[long-read-tools @long_read_tools]

...
- error correction: HERO, HERRO,
- transcriptomics: MisER, Longcell, LAPA, CTAT-LR-Fusion, CTAT-Mutations, rnaSPAdes, rpvg, MAJIQ-L, Isosceles,
- QC: Mana
- other: Decoil, slow5curl, QUILT, eXNVerify, SAMOSA-ChAAT, FMAlign2, bed-bugs

[long-read-tools @long_read_tools]

No fewer than 37 tools added!
- variant calling: Severus, DeepSomatic, Clair3-MP, ClairS-TO, HiFiHLA, Napu, invMap, MacroHapCaller
- assembly: CRAQ, VRP Assembler, RAFT, metaMDBG
- basemods: m6ABasecaller, SingleMod, PsiNanopore, kineticsTools, Xron, ccsmethphase, IL-AD
...

[Liz Tseng @Magdoll]

@PacBio 12/ long-read RNA-Seq #bioinformatics is where it is today becuz of early adopters like @anaconesa @FairlieReese including those originally dev for ONT works on PacBio too!

Here’s an abbreviated list of compatible tool to get you started

https://t.co/2jqQU0bGIn

[Ryan Wick @rrwick]

New blog post:
https://t.co/Kvkkb9ucNu

I revisit the question of ONT-only accuracy for bacterial genomes, and things have improved a lot since I last looked at this about six months ago!

[long-read-tools @long_read_tools]

@alt_spliced @tangming2005 you can also check out @JonathanGoeke lab’s curated list https://t.co/SdvbBdRF95

[long-read-tools @long_read_tools]

Loads of new tools, for a new total of 834!
Reminder: in the table, you can add "Pub Dates" and sort by most recent https://t.co/ObKIHLeV43

[Jonathan Göke @JonathanGoeke]

Long reads are one of the greatest innovations for RNA profiling as they help to identify individual isoforms. But… what about long reads that don't perfectly match reference annotations?

Very happy to share our answer to this question - bambu! https://t.co/o6OLseIwHa 1/n

[Chris Seymour @iiSeymour]

Huge dorado release 🎉

- 1.4x simplex perf HAC/SUP on A100
- 5khz v4.2 models
- All context 5mC, 6mA models
- Significantly faster duplex calling
- Duplex pairing handled automatically
- BAM output
- Aligned output via minimap2

#nanoporeconf

https://t.co/4LMdfUxKT9

[long-read-tools @long_read_tools]

Fresh batch of 10 tools, try them while they’re hot 🥐:
- SVs (Cue, cnnLSV, SVsearcher)
- BaseMods (PAPET, 6mA-Sniper, Magnipore)
- Transcriptomics (nf-core/isoseq, Pbfusion)
- Metagenomics (IDseq)
- Polishing (JASPER)
Updated dois for nPore, NextDenovo, TrEMOLO, Insplico, BLAZE

[long-read-tools @long_read_tools]

do we need to add ChatGPT? 🤔

[long-read-tools @long_read_tools]

- and pubs for Methylmap, VG, buttery_eel, MasterOfPores

[long-read-tools @long_read_tools]

lots of tools added:
- nanoHiMe, Pigeon, ESPRESSO, DeBreak, RawHash, Telomap, VAG, disCoverage, HiFiAdapterFilt, CrossStitch, WeFaceNano, ntLink, Hare_and_Tortoise(HAT), Nanospring, JACUSA2, Penguin, scNanoGPS, paraphrase, R2Dtool, stRain, LRphase

[Chris Saunders @ctsa11]

For anyone wanting to explore their @PacBio SMRT kinetics data, we've recently helped to update IGV with visualization support for both HiFi and subread bams. Here's an example highlighting m6A around a Dam Mtase site in E coli. Big thanks to @igvteam for this.

[long-read-tools @long_read_tools]

Long-read sequencing is Method of the Year! Only thanks to all the great tools that make the most of those light flashes and current squiggles
https://t.co/OLSdxIPiTy

[long-read-tools @long_read_tools]

New year new tools!
- AccuVIR (viral assembly)
- strainFlye, CZ ID (metagenomics)
- annotate_my_genomes, NanopoReaTA (transcriptomics)
- NanoSNP, delInsCaller, SVseq3 (variation)
... and Freddie, SVDSS, RagTag published

[long-read-tools @long_read_tools]

and m6Anet, VeChat, HAT now published

[long-read-tools @long_read_tools]

708! In this update:
- Sketching (long read classification)
- HISS (RenSeq analysis, plant disease resistance)
- HaploDMF (viral haplotype assy)
- T1K (K IR/HLA��genotyping)
- NanoBlot (3rd gen seq -> blots!!)
- DeepSelectNet (adaptive sampling ONT)
- WarpSTR (STR analysis)