# Latest **URL:** https://community.artic.network/latest.md [Latest](https://community.artic.network/latest.md) · [Categories](https://community.artic.network/categories.md) --- ## [Welcome to Discourse](https://community.artic.network/t/welcome-to-discourse/7)
**Author:** [@system](https://community.artic.network/u/system)\ **Replies:** 0\ **Last updated:** [14 March 2020 11:08 UTC](https://community.artic.network/t/welcome-to-discourse/7 "2020-03-14T11:08:08Z")
Welcome to the ARTIC real-time genomic surveillance community. Here, the ARTIC team will post updates and information about the ARTIC laboratory, bioinformatics and phylogenetics methods we are developed. More broadly th… --- ## [Fieldbioinformatics updated to 1.6.2](https://community.artic.network/t/fieldbioinformatics-updated-to-1-6-2/562)
**Author:** [@Sam-W](https://community.artic.network/u/Sam-W)\ **Replies:** 0\ **Last updated:** [3 April 2025 11:26 UTC](https://community.artic.network/t/fieldbioinformatics-updated-to-1-6-2/562 "2025-04-03T11:26:22Z")
\> Fieldbioinformatics updated to 1.6.2 Fieldbioinformatics has been the first line recommendation by the artic network for generation of consensus sequences from Nanopore viral amplicon sequencing data since the we… --- ## [ARTIC Multiplex PCR (Full pathogens list)](https://community.artic.network/t/artic-multiplex-pcr-full-pathogens-list/494)
**Author:** [@Kess\_Rowe](https://community.artic.network/u/Kess_Rowe)\ **Replies:** 1\ **Last updated:** [23 August 2024 12:54 UTC](https://community.artic.network/t/artic-multiplex-pcr-full-pathogens-list/494 "2024-08-23T12:54:48Z")
Below is a living excel spreadsheet of pathogens that have been sequenced using Primal Scheme approach to produce tiled amplicons for multiplex PCR. The spreadsheet cites the first use of the technique for various major … --- ## [Scheme release: artic-sars-cov2/400/v5.4.2](https://community.artic.network/t/scheme-release-artic-sars-cov2-400-v5-4-2/546)
**Author:** [@chriken](https://community.artic.network/u/chriken)\ **Replies:** 0\ **Last updated:** [5 August 2024 17:24 UTC](https://community.artic.network/t/scheme-release-artic-sars-cov2-400-v5-4-2/546 "2024-08-05T17:24:15Z")
Summary Our collaborators at the British Columba Centre for Disease Control (BCCDC), have updated artic-sars-cov2/400/v5.3.2 scheme to handle mutations found in the currently dominate lineages (JN.1). Spike in primers … --- ## [Overview of the LoCost SARS-CoV-2 protocol](https://community.artic.network/t/overview-of-the-locost-sars-cov-2-protocol/542)
**Author:** [@Lauren](https://community.artic.network/u/Lauren)\ **Replies:** 0\ **Last updated:** [26 July 2024 14:49 UTC](https://community.artic.network/t/overview-of-the-locost-sars-cov-2-protocol/542 "2024-07-26T14:49:45Z")
LoCost overview The LoCost workflow provides laboratory and bioinformatics protocols for whole genome amplicon sequencing of SARS-CoV-2. It has been designed to be used with the Oxford Nanopore (ONT) MinION sequencer, d… --- ## [SARS-CoV-2 version 5.3.2 scheme release](https://community.artic.network/t/sars-cov-2-version-5-3-2-scheme-release/462)
**Author:** [@scalene](https://community.artic.network/u/scalene)\ **Replies:** 12\ **Last updated:** [18 June 2024 14:51 UTC](https://community.artic.network/t/sars-cov-2-version-5-3-2-scheme-release/462 "2024-06-18T14:51:42Z")
Introduction Deciding when to release a new primer scheme is always a difficult decision because we want continuity but don’t want genomes with dropouts caused by primer problems. ARTIC v4/4.1 has been the recommended s… --- ## [A Beginner's Guide to ARTIC](https://community.artic.network/t/a-beginners-guide-to-artic/531)
**Author:** [@Lauren](https://community.artic.network/u/Lauren)\ **Replies:** 0\ **Last updated:** [9 May 2024 14:22 UTC](https://community.artic.network/t/a-beginners-guide-to-artic/531 "2024-05-09T14:22:04Z")
What is ARTIC? ARTIC comprises a collection of open-access resources, both for laboratory work and data processing and analysis, to enable real-time molecular epidemiology for pathogen surveillance and outbreak response… --- ## [Pre-designed Primer Schemes](https://community.artic.network/t/pre-designed-primer-schemes/530)
**Author:** [@Lauren](https://community.artic.network/u/Lauren)\ **Replies:** 0\ **Last updated:** [9 May 2024 14:05 UTC](https://community.artic.network/t/pre-designed-primer-schemes/530 "2024-05-09T14:05:00Z")
For an up-to-date list of pre-designed primer schemes for various pathogens (e.g. SARS-Cov-2, Ebola, Measles), check out the primal scheme website --- ## [Marburg 2023 primer scheme release](https://community.artic.network/t/marburg-2023-primer-scheme-release/479)
**Author:** [@scalene](https://community.artic.network/u/scalene)\ **Replies:** 0\ **Last updated:** [16 February 2023 15:00 UTC](https://community.artic.network/t/marburg-2023-primer-scheme-release/479 "2023-02-16T15:00:30Z")
We have generated a Marburg virus scheme in response to recent reports of an outbreak in Equatorial Guinea. We attempted to make a pan-MARV scheme incorporating all the publicly available genomes but the ‘primer clouds’ … --- ## [Erroneous Mutations Associated with 64\_L-60\_R Primer-Dimer in ARTIC 4/4.1 ](https://community.artic.network/t/erroneous-mutations-associated-with-64-l-60-r-primer-dimer-in-artic-4-4-1/419)
**Author:** [@Sam-W](https://community.artic.network/u/Sam-W)\ **Replies:** 0\ **Last updated:** [31 March 2022 10:27 UTC](https://community.artic.network/t/erroneous-mutations-associated-with-64-l-60-r-primer-dimer-in-artic-4-4-1/419 "2022-03-31T10:27:55Z")
Erroneous Mutations Associated with 64\_L-60\_R Primer-Dimer in ARTIC 4/4.1 Report prepared by: Sam Wilkinson, Natalie Groves, Josh Quick, Nick Loman Recently 664 (correct as of 2022-03-29) SARS-CoV-2 sequences have been… --- ## [SARS-CoV-2 V4.1 update for Omicron variant](https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342)
**Author:** [@scalene](https://community.artic.network/u/scalene)\ **Replies:** 0\ **Last updated:** [1 December 2021 15:17 UTC](https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342 "2021-12-01T15:17:29Z")
Introduction Multiplex PCR relies on gene-specific primers to enrich for viral sequences, and this makes it useful for generating viral genomes sequencing from clinical samples with a complex background. This also, howe… --- ## [SARS-CoV-2 version 4 scheme release](https://community.artic.network/t/sars-cov-2-version-4-scheme-release/312)
**Author:** [@scalene](https://community.artic.network/u/scalene)\ **Replies:** 0\ **Last updated:** [24 June 2021 12:05 UTC](https://community.artic.network/t/sars-cov-2-version-4-scheme-release/312 "2021-06-24T12:05:04Z")
Motivation ARTIC V3 primers have been the workhorse of SARS-CoV-2 sequencing for 15 months and have under various guises been used in the production of a large proportion of the ~2M genomes that have been deposited in G… --- ## [Aric MinION pipeline compaible with new demultiplexing - Nanopolish with fast5 in subfolder](https://community.artic.network/t/aric-minion-pipeline-compaible-with-new-demultiplexing-nanopolish-with-fast5-in-subfolder/286)
**Author:** [@weehzer](https://community.artic.network/u/weehzer)\ **Replies:** 1\ **Last updated:** [5 May 2021 11:44 UTC](https://community.artic.network/t/aric-minion-pipeline-compaible-with-new-demultiplexing-nanopolish-with-fast5-in-subfolder/286 "2021-05-05T11:44:36Z")
Hi, the new versions of MinKNOW allows to demultiplex with the option “requiring barcodes at both ends”, which is what we need for the artic pipeline. However, recently not just the fastq files but also the fast5 files… --- ## [Medaka/Longshot pipeline](https://community.artic.network/t/medaka-longshot-pipeline/107)
**Author:** [@nick](https://community.artic.network/u/nick)\ **Replies:** 1\ **Last updated:** [23 April 2021 12:17 UTC](https://community.artic.network/t/medaka-longshot-pipeline/107 "2021-04-23T12:17:47Z")
For those that have been using 1.1.0-rc1 of the pipeline over the past week or so with the experimental Medaka mode, it has been noted by two users that the Longshot step can occasionally filter genuine variants (detecte… --- ## [Artic minion pipeline with 2 sequencing runs and 2 sets of tiling primers](https://community.artic.network/t/artic-minion-pipeline-with-2-sequencing-runs-and-2-sets-of-tiling-primers/222)
**Author:** [@AK\_Virus](https://community.artic.network/u/AK_Virus)\ **Replies:** 1\ **Last updated:** [6 August 2020 20:31 UTC](https://community.artic.network/t/artic-minion-pipeline-with-2-sequencing-runs-and-2-sets-of-tiling-primers/222 "2020-08-06T20:31:44Z")
My lab developed their own set of tiling primers, which while problematic in some ways could potentially fill in some of the low coverage areas we’re getting with the artic V3 tiling primers. I’m trying to run the artic… --- ## [Two-barcode demux requirement](https://community.artic.network/t/two-barcode-demux-requirement/215)
**Author:** [@jvolkening](https://community.artic.network/u/jvolkening)\ **Replies:** 4\ **Last updated:** [14 July 2020 21:53 UTC](https://community.artic.network/t/two-barcode-demux-requirement/215 "2020-07-14T21:53:42Z")
Hello all, This is a duplicate of a question I posted to the ARTIC pipeline GitHub issues (at github.com/artic-network/fieldbioinformatics/issues/52 – can’t actually link because I’m too new!). in case there are additio… --- ## [Post Rampart informatics?](https://community.artic.network/t/post-rampart-informatics/205)
**Author:** [@amazonmatt](https://community.artic.network/u/amazonmatt)\ **Replies:** 0\ **Last updated:** [20 June 2020 00:11 UTC](https://community.artic.network/t/post-rampart-informatics/205 "2020-06-20T00:11:53Z")
If we run rampart, can we “skip ahead” in the informatics? Or should we re-base call the Fast5 and re-demux, per the bioinformatics SOP. It seems redundant, but it also seems like it what people are doing? --- ## [Agilent gel images](https://community.artic.network/t/agilent-gel-images/203)
**Author:** [@spinlerj](https://community.artic.network/u/spinlerj)\ **Replies:** 0\ **Last updated:** [19 June 2020 12:24 UTC](https://community.artic.network/t/agilent-gel-images/203 "2020-06-19T12:24:50Z")
We use Agilent chips for QCing amplified products prior to sequencing. Does anyone have gel images from Agilent chips for the covid19 PCR tiling products they’d be willing to share? We’d like to get an idea how well our … --- ## [V3 primer availability](https://community.artic.network/t/v3-primer-availability/123)
**Author:** [@scalene](https://community.artic.network/u/scalene)\ **Replies:** 0\ **Last updated:** [13 April 2020 15:51 UTC](https://community.artic.network/t/v3-primer-availability/123 "2020-04-13T15:51:08Z")
\*\* ARTIC nCoV-2019 V3 primer pool availability \*\* In the last post I alluded to the fact that ARTIC have been working with IDT to manufacture ARTIC nCoV-2019 V3 primer pools as a pre-pooled, ready to use formulation. I… --- ## [Links to raw (FAST5/FASTQ) data for ARTIC protocol](https://community.artic.network/t/links-to-raw-fast5-fastq-data-for-artic-protocol/17)
**Author:** [@nick](https://community.artic.network/u/nick)\ **Replies:** 1\ **Last updated:** [20 May 2020 12:26 UTC](https://community.artic.network/t/links-to-raw-fast5-fastq-data-for-artic-protocol/17 "2020-05-20T12:26:18Z")
Due to popular request on Twitter, I am collecting some links to raw data for ARTIC protocol runs in this post. Please do post additional datasets you might wish to share. The ARTIC pipeline should not generate much or … --- ## [Update link to protocols.io](https://community.artic.network/t/update-link-to-protocols-io/153)
**Author:** [@martinalexsmith](https://community.artic.network/u/martinalexsmith)\ **Replies:** 7\ **Last updated:** [14 May 2020 22:39 UTC](https://community.artic.network/t/update-link-to-protocols-io/153 "2020-05-14T22:39:03Z")
Hello folks, We just ran the ARTIC protocol on some samples, but noticed there is a V2 version of the protocol which isn’t obvious to find from the website. The V1 version yielded lots of double barcode events and a non… --- ## [Dropout of amplicon 64](https://community.artic.network/t/dropout-of-amplicon-64/167)
**Author:** [@Claire](https://community.artic.network/u/Claire)\ **Replies:** 2\ **Last updated:** [8 May 2020 02:14 UTC](https://community.artic.network/t/dropout-of-amplicon-64/167 "2020-05-08T02:14:49Z")
Anyone seeing dropout of amplicon 64? Have you been able to fix it? TIA --- ## [Any possible speedup of real-time basecalling](https://community.artic.network/t/any-possible-speedup-of-real-time-basecalling/160)
**Author:** [@afadeew](https://community.artic.network/u/afadeew)\ **Replies:** 1\ **Last updated:** [7 May 2020 18:30 UTC](https://community.artic.network/t/any-possible-speedup-of-real-time-basecalling/160 "2020-05-07T18:30:25Z")
Hi all, I expirienced a problem with real-time basecalling for RAMPART. I am using MinKnow 19.12.5 with built-in Guppy 3.2.10 on Linux Mint 19.3. When I start a run and choose “Basecalling ON” option, basecalling start… --- ## [Human Read Removal](https://community.artic.network/t/human-read-removal/157)
**Author:** [@cazzlewazzle89](https://community.artic.network/u/cazzlewazzle89)\ **Replies:** 0\ **Last updated:** [28 April 2020 15:16 UTC](https://community.artic.network/t/human-read-removal/157 "2020-04-28T15:16:53Z")
Hi All, We are using the v3 protocol for sequencing on ONT (minion/gridion). I know there will be minimal risk of host DNA sequencing but are there any recommendations to ensure this is the case before raw data is uplo… --- ## [The ARTIC workflows with Illumina / short read sequencing](https://community.artic.network/t/the-artic-workflows-with-illumina-short-read-sequencing/58)
**Author:** [@adahl](https://community.artic.network/u/adahl)\ **Replies:** 12\ **Last updated:** [23 April 2020 11:28 UTC](https://community.artic.network/t/the-artic-workflows-with-illumina-short-read-sequencing/58 "2020-04-23T11:28:06Z")
Dear all, For Virus sequencing do you know of any activities to use your V3 priming set with Illumina? We started working on it and would be interest in exchanging ideas. Cheers and many thanks in advance!!! Andreas --- ## [Recommendations for GPU Laptops](https://community.artic.network/t/recommendations-for-gpu-laptops/139)
**Author:** [@pthielen](https://community.artic.network/u/pthielen)\ **Replies:** 1\ **Last updated:** [22 April 2020 11:03 UTC](https://community.artic.network/t/recommendations-for-gpu-laptops/139 "2020-04-22T11:03:57Z")
We have historically used fast basecalling on laptops for small scale ONT work, but ultimately would like to use high accuracy basecalling (HAC) going forward. We have therefore moved to HAC (gridion) for our production … --- ## [Ct higher than 35](https://community.artic.network/t/ct-higher-than-35/136)
**Author:** [@Emanuela](https://community.artic.network/u/Emanuela)\ **Replies:** 1\ **Last updated:** [20 April 2020 09:31 UTC](https://community.artic.network/t/ct-higher-than-35/136 "2020-04-20T09:31:48Z")
Hi, I have some RNA sample with ct\>35. Do you suggest to proceed with 11ul or do you recommend another approach? Thanks in advance --- ## [Run Artic on HPC cluster that is not conda-friendly](https://community.artic.network/t/run-artic-on-hpc-cluster-that-is-not-conda-friendly/117)
**Author:** [@ArnieBerg](https://community.artic.network/u/ArnieBerg)\ **Replies:** 2\ **Last updated:** [18 April 2020 17:51 UTC](https://community.artic.network/t/run-artic-on-hpc-cluster-that-is-not-conda-friendly/117 "2020-04-18T17:51:53Z")
Is there an alternative installation and deployment Artic package that does not require conda? The High Performance Computing cluster I would like to deploy on does not support conda. --- ## [PCR extension time](https://community.artic.network/t/pcr-extension-time/52)
**Author:** [@helena\_ss](https://community.artic.network/u/helena_ss)\ **Replies:** 4\ **Last updated:** [15 April 2020 06:33 UTC](https://community.artic.network/t/pcr-extension-time/52 "2020-04-15T06:33:42Z")
Is 5 min extension time really necessary for 400bp fragments? We’ve been trying to do the whole protocol in one day and it’s been stretching to 13 hours. If we can save time at any step, that would help! --- ## [nCoV-2019 Version 3 Amplicon Release](https://community.artic.network/t/ncov-2019-version-3-amplicon-release/19)
**Author:** [@nick](https://community.artic.network/u/nick)\ **Replies:** 8\ **Last updated:** [13 April 2020 15:00 UTC](https://community.artic.network/t/ncov-2019-version-3-amplicon-release/19 "2020-04-13T15:00:17Z")
nCoV-2019/nCoV-2019 Version 3 Amplicon Set PDF version of this announcement here: https://artic.network/resources/ncov/ncov-amplicon-v3.pdf The ARTIC project released a protocol for sequencing nCoV-2019 on January 22n… [Next page](https://community.artic.network/latest.md?page=1)