Nextstrain

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19 Jan, 11 tweets, 8 min read

We are always looking for ways to make things better, more intuitive, & more helpful at Nextstrain! Some of you may have already noticed that we recently added a bunch of great new features - but in case you didn't, let's explore them!

1/11

First, if you're a regular user you'll remember the fun of extra-long legends even when zoomed in...

Now, the legend will only show what's visible on the map, making it much more useful!

(Works with colourings like genotype, too!)

2/11

When using Nextstrain we often want to examine 2 things at once - until now that was sometimes difficult!

Now it's a little easier - you can change the tip-labels from the default 'strain', so that you can combine colouring & tip labels to show different things!

3/11

With the recent type-to-filter function it's easier than ever to narrow down to just the sequences you want - but you're often still very far away!

A new 'Zoom to Selected' button will take you right in close to exactly what you're interested in looking at!

4/11

If you commonly download trees from Nextstrain you'll be happy to learn we've improved how this works!

Downloaded trees now reflect the subtree visible & you can now download annotated Nexus format that works in FigTree! (Note the view is 'upside down' between the 2 pics!)

5/11

Use drag-&-drop metadata to add extra info to builds? We've updated this too!

See the docs below for the details - it's now easier to see which tips added metadata & to add more types of data! (If you don't know about this feature - check it out!)

6/11

docs.nextstrain.org/projects/auspi…

This is a little more subtle, but can still be very useful:

Previously, our frequency charts only had 1 point a month, sometimes leading to choppy graphs. We've improved this, so graphs are smoother & project less extremely into the future!

(Old on left, new on right!)

7/11

Finally, we've vastly improved how we can show off the many #SARSCoV2 Nextstrain builds people are maintaining, all over the world! See the new map (link below)!

Click to zoom in on regions with many builds & mouse-over dots to find out more!

8/11

nextstrain.org/sars-cov-2/#bu…

It's easy to add your own build to this map! (& we'd love to have it up to help others find it!) Just submit a Pull Request to our nextstrain.org repository - you can find how to do this at the link below!

9/11

docs.nextstrain.org/en/latest/guid…

You can read about all of our latest updates in our Changelog (linked below).

We hope these updates make Nextstrain even more useful for your exploration, research, & analysis!

10/11

docs.nextstrain.org/projects/auspi…

These updates are thanks to great ideas & hard work from many Nextstrain team members, in particular from @hamesjadfield @wcassias @eliasharkins @trvrb & Jover Lee! 🙏🏻🚀

11/11

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More from @nextstrain

Nextstrain

@nextstrain

19 Jan

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 7368 #COVID19 #SARSCoV2 sequences!

Seqs from Nigeria (8) & South Africa (101) on nextstrain.org/ncov/africa.

(Thanks to @NCDCgov, @krisp_news, @rjlessells, @Tuliodna, @EduanWilkinson, @nhls_sa)

1/9

@GISAID @NCDCgov @krisp_news @rjlessells @Tuliodna @EduanWilkinson @nhls_sa You can find the new sequences from Australia (1), Brazil (36), Ecuador (23) and Peru (1) on nextstrain.org/ncov/oceania and nextstrain.org/ncov/south-ame….

(Thanks to @NSWHPathology, @WestSydHealth, @Sydney_Uni, @UFCSPA, Instituto Adolfo Lutz, @ispch, @INS_Peru)

2/9

@GISAID @NCDCgov @krisp_news @rjlessells @Tuliodna @EduanWilkinson @nhls_sa @NSWHPathology @WestSydHealth @Sydney_Uni @UFCSPA @ispch @INS_Peru Check out new sequences from Bangladesh (5), India (48), Indonesia (2), Myanmar (1) & Singapore (20) on nextstrain.org/ncov/asia.

(Thanks to Genomic Research Lab at #BCSIR, @gbrc_gujarat, #virologynimhans, @virology_chitra, DMR Myanmar, NIHRD Indonesia, NCID NPHL Singapore)

3/9

Nextstrain

@nextstrain

13 Jan

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 9898 new #COVID19 #SARSCoV2 sequences!

New sequences from Egypt (17) & Tunisia (10) on nextstrain.org/ncov/africa

(Thanks to @mohpegypt, MCL Egypt, @univtunismanar, Ministry of Health Tunisia)

1/11

@GISAID @mohpegypt @univtunismanar Check out the new sequences from Australia (76) and New Zealand (18) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology, @WestSydHealth, @Sydney_Uni, #PathWest Laboratory Medicine, @WAHealth, @ESRNewZealand, @MathStorey, @Joepdl, @sciolato)

2/11

@GISAID @mohpegypt @univtunismanar @NSWHPathology @WestSydHealth @Sydney_Uni @WAHealth @ESRNewZealand @MathStorey @Joepdl @sciolato New sequences from Brazil (18), Chile (353), Colombia (19) and Ecuador (1) can be found on nextstrain.org/ncov/south-ame….

(Thanks to @FiocruzAmazonia, @MountSinaiNYC, @uandresbello, @INSColombia, @paulcarald, @BelenPradoV, @juanjogl89, @USFQ_Ecuador, @IMUSFQ, @B_Gutierrez_G)

3/11

Nextstrain

@nextstrain

11 Jan

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 15266 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Australia (264) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology, @WestSydHealth, @Sydney_Uni, MDU-PHL, VIDRL)

1/9

@GISAID @NSWHPathology @WestSydHealth @Sydney_Uni New sequences from Guinea (6) can be seen on nextstrain.org/ncov/africa.

(Thanks to @transvihmi, @ird_fr, @Inserm, @umontpellier, @CerfigGuinee, @Alfa_kabi)

2/9

@GISAID @NSWHPathology @WestSydHealth @Sydney_Uni @transvihmi @ird_fr @Inserm @umontpellier @CerfigGuinee @Alfa_kabi New sequences from India (5), Indonesia (13), Japan (4), Pakistan (36) and Sri Lanka (10) below.

(Thanks to FMR India NIHRD Indonesia National Institute of Infectious Diseases Japan Jamil-ur-Rahman Center Dr. Panjwani Center @usjp @chandi2012 @GMalavige @DinukaaR)

3/9

Nextstrain

@nextstrain

9 Jan

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 4060 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Australia (2) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology)

1/6

@GISAID @NSWHPathology You can find the new sequences from Morocco (10), Bangladesh (155), Indonesia (6) and Israel (182) on nextstrain.org/ncov/africa and nextstrain.org/ncov/asia.

(Thanks to @um5rabat, @SolutionDna, @gksavarHQ, NIHRD Indonesia, Israel Central Virology Lab)

2/6

@GISAID @NSWHPathology @um5rabat @SolutionDna @gksavarHQ Check out the new sequences from Argentina (1) and Brazil (34) on nextstrain.org/ncov/south-ame….

(Thanks to @SADI_ORG, @lnccientifica, Instituto Adolfo Lutz)

3/6

Nextstrain

@nextstrain

7 Jan

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 2963 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Australia (105) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology, @WestSydHealth, @Sydney_Uni, @SAHealth)

1/6

@GISAID @NSWHPathology @WestSydHealth @Sydney_Uni @SAHealth You can find the new sequences from Brazil (80), Botswana (6) and Morocco (2) on nextstrain.org/ncov/south-ame… and nextstrain.org/ncov/africa.

(Thanks to @lnccientifica, @BITRI1640, @um5rabat)

2/6

@GISAID @NSWHPathology @WestSydHealth @Sydney_Uni @SAHealth @lnccientifica @BITRI1640 @um5rabat You can see the new sequences from Bangladesh (15), Lebanon (4), Singapore (16) and Thailand (30) below.

(Thanks to @chrfbd @senjutisaha @ChrfSaha @SajibMSI @MalakerRoly @BinZabed @HafizShakil703 @msohag10 @LAUArtsSciences @mysgh NCID NPHL Singapore @thailandnih @pr_moph)

3/6

Nextstrain

@nextstrain

7 Jan

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 1513 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Algeria (14) and Nigeria (2) on nextstrain.org/ncov/africa.

(Thanks to @Pasteur_Algerie @institutpasteur, @NCDCgov)

1/5

@GISAID @Pasteur_Algerie @institutpasteur @NCDCgov You can find the new sequences from Indonesia (17) and Oman (2) on nextstrain.org/ncov/asia.

(Thanks to @eijkman_inst, @KemenristekBRIN, @SQU_Info @microlab_squ)

2/5

@GISAID @Pasteur_Algerie @institutpasteur @NCDCgov @eijkman_inst @KemenristekBRIN @SQU_Info @microlab_squ You can see the new sequences from the USA (590) on nextstrain.org/ncov/north-ame….

(Thanks to @lapublichealth, @delaware_gov, @HealthyFla, BioInfo Experts LLC, @sabeti_lab, @broadinstitute, @MichiganHHS, @NMDOH, @unrmed, @HealthNYGov, @TexasDSHS, Wyoming Public Health Lab)

3/5

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