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- Abhi@abhinav
Abhi bookmarked Peregrine & SHIMMER Genome Assembly Toolkit 1107 days ago

Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...

https://github.com/cschin/Peregrine
- Abhi@abhinav
Abhi bookmarked Rules for Pango Lineage ! 1109 days ago

All the rules to classify a Lineage ! https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/

https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary posted to the wire 1110 days ago

A modeling study predicts that there is a “realistic possibility” that B.1.617.2 is 60% more transmissible than the Alpha variant (B.1.1.7).
- Abhi@abhinav
Abhi bookmarked Corona Virus Genome and Data Download ! 1110 days ago

Genes and its related metadata could be found on https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/

https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/
- Abhi@abhinav
Abhi bookmarked Corona Virus Literature ! 1110 days ago

LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 201482 (and growing)...

https://www.ncbi.nlm.nih.gov/research/coronavirus/
- Jit@jit.aber
Jit bookmarked Refseq viraal genome sequences ! 1112 days ago

List of all viruses on NCBI https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/
- Jit@jit.aber
Jit bookmarked fastv - detect virus 1112 days ago

fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect...

https://github.com/OpenGene/fastv
- Jit@jit.aber
Jit bookmarked UniqueKMER 1112 days ago

Generate unique k-mers for every contig in a FASTA file. Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands).

https://github.com/OpenGene/UniqueKMER
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary created a new bio-script Extract fasta header with ids ! 1113 days ago
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary published a blog post Illumina based assembly pipeline steps ! 1113 days ago

Genome assembly pipeline !
- Abhi@abhinav
Abhi bookmarked Pangolin tutorial ! 1113 days ago

This is a tutorial for using the Pangolin Web Application. For information on using the command line tool, please visit the command line tool usage page. https://cov-lineages.org/resources/pangolin/tutorial.html

https://cov-lineages.org/resources/pangolin/tutorial.html
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary posted to the wire 1113 days ago

Chloropleth maps http://helenjacksonanalytic.co.uk/EW_prop_price.html and https://www.ucas.com/corporate/data-and-analysis/ucas-undergraduate-releases/equality-he-reports #Chloropleth
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary posted to the wire 1113 days ago

Best Javascript charts https://www.monterail.com/blog/javascript-libraries-data-visualization #Javascript #Chats
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary posted to the wire 1113 days ago

Deploy dashboard on server https://dash.plotly.com/deployment #Dashboard #Deploy #Server
- Jit@jit.aber
Jit commented on a bookmark ncbi-datasets-cli -- Quickstart: command line tools ! 1116 days ago

(base) [jnarayan@hn1 TOOLS]$ curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets' % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed100 13.8M 100 13.8M...
- Jit@jit.aber
Jit bookmarked ncbi-datasets-cli -- Quickstart: command line tools ! 1116 days ago

Install and use the NCBI Datasets command line tools The NCBI Datasets datasets command line tools are datasets and dataformat . Use datasets to download biological sequence data across all domains of life from...

https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/
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- Jit@jit.aber
  
  Jit 1116 days ago
  (base) [jnarayan@hn1 TOOLS]$ curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets'
  % Total % Received % Xferd Average Speed Time Time Time Current
  Dload Upload Total Spent Left Speed
  100 13.8M 100 13.8M 0 0 440k 0 0:00:32 0:00:32 --:--:-- 425k
  (base) [jnarayan@hn1 TOOLS]$ curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/dataformat'
  % Total % Received % Xferd Average Speed Time Time Time Current
  Dload Upload Total Spent Left Speed
  100 11.4M 100 11.4M 0 0 509k 0 0:00:23 0:00:23 --:--:-- 558k
  (base) [jnarayan@hn1 TOOLS]$ chmod +x datasets dataformat
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary created a new bio-script Omicron Sequences accession number ! 1121 days ago
- Neel@neelam
Neel bookmarked MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization 1122 days ago

MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw...

https://github.com/linzhi2013/MitoZ
- Jit@jit.aber
Jit created a new bio-script Run Pango on your multifasta file ! 1123 days ago
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary created a new bio-script Extract fasta sequences with ids in another file ! 1125 days ago

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