# Bioinformatics **URL:** https://community.artic.network/c/bioinformatics/5.md [Latest](https://community.artic.network/latest.md) · [Categories](https://community.artic.network/categories.md) --- ## [About the Bioinformatics category](https://community.artic.network/t/about-the-bioinformatics-category/12)
**Author:** [@nick](https://community.artic.network/u/nick)\ **Replies:** 0
--- ## [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… --- ## [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? --- ## [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 … --- ## [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… --- ## [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 … --- ## [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. --- ## [Bcftools consensus error](https://community.artic.network/t/bcftools-consensus-error/112)
**Author:** [@josephfauver](https://community.artic.network/u/josephfauver)\ **Replies:** 2\ **Last updated:** [8 April 2020 21:34 UTC](https://community.artic.network/t/bcftools-consensus-error/112 "2020-04-08T21:34:23Z")
Hi all- First of all- thanks for setting up this discussion board, it is incredibly helpful. We have been using the ARTIC lib prep and bioinformatics protocol for all of our SARS-nCoV-2 sequencing and it has worked gre… --- ## [RAMPART v1.1.0 released](https://community.artic.network/t/rampart-v1-1-0-released/69)
**Author:** [@james](https://community.artic.network/u/james)\ **Replies:** 4\ **Last updated:** [1 April 2020 22:01 UTC](https://community.artic.network/t/rampart-v1-1-0-released/69 "2020-04-01T22:01:12Z")
A new version of RAMPART, our software for analyzing nanopore data in real-time, is now available. This brings a number of major changes which should help with SARS-CoV-2 analyses. There are no changes to how RAMPART is… --- ## [Minimum coverage required?](https://community.artic.network/t/minimum-coverage-required/49)
**Author:** [@helena\_ss](https://community.artic.network/u/helena_ss)\ **Replies:** 1\ **Last updated:** [30 March 2020 20:11 UTC](https://community.artic.network/t/minimum-coverage-required/49 "2020-03-30T20:11:40Z")
The pipeline seems to trim coverage to mean 400x ish in \*trimmed.sorted.bam, probably with \>artic minion --normalise 200 ? Is this a minimum for submission to https://gisaid.org? Have you set minimum coverage for accur… --- ## [How to accelerate the demultiplex speed?](https://community.artic.network/t/how-to-accelerate-the-demultiplex-speed/42)
**Author:** [@indexofire](https://community.artic.network/u/indexofire)\ **Replies:** 3\ **Last updated:** [30 March 2020 03:30 UTC](https://community.artic.network/t/how-to-accelerate-the-demultiplex-speed/42 "2020-03-30T03:30:57Z")
ARTIC tools use porechop to re-demultiplexing the samples obligatorily. However it take too much time in my SERVER like 8G fastq per day. Anyway to accelerate the process?