Tag: Magic-BLAST

NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021)

NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021)

Come visit us virtually to learn about new NCBI data access, tools and best practices at the Bioinformatics Open Science Conference  part of the ISMB/ECCB online conference from July 29 – 30, 2021. We will be presenting virtual posters on NCBI resources, offering a Birds of a Feather discussion, and participating in the BOSC  (CoFest) following the conference where you can take part in a hands-on evaluation of ElasticBLAST.

NCBI Posters, July 29, 2021, 11:20 – 12:20 PM EDT

All posters will be presented on Thursday afternoon. You can see complete abstracts on the ISMB/ECCB BOSC schedule.

Nuala O’Leary will talk about NCBI Datasets, a new resource for fast, easy access to NCBI sequence data.  You will learn about the new interface and new tools to access reference genomes, genes, and orthologs using web-based and programmatic tools.

Adelaide Rhodes will present Open access NCBI cloud resources to accelerate scientific insights where you can learn about recent developments in transferring > 20 petabytes of NCBI Sequence Read Archive (SRA) data to the cloud.

Deacon Sweeney will describe the web RAPT service for assembling and annotating bacterial genomes at the click of a button in RAPT, The Read assembly and Annotation Pipeline Tool: building a prokaryotic genome annotation package for users of all backgrounds.

Roberto Vera Alvarez will talk about best practices for using cloud tools for transcriptomics in his poster Transcriptome annotation in the cloud: complexity, best practices, and cost.

Greg Boratyn will discuss improvements to the BLAST-based short read aligner, Magic-Blast, in Recent improvements in Magic-BLAST 1.6.

Visit Christiam Camacho’s poster ElasticBLAST: Using the power of the cloud to speed up science to get an introduction to  ElasticBLAST, a Kubernetes-based approach for high throughput BLAST tasks. Join us following the conference in the CoFest to try out ElasticBLAST yourself and provide input. See the section on the CoFest below and our companion post.

Birds of a Feather, July 29, 2021, 11:20 – 12:20 PM EDT

We will host a Birds of Feather public feedback session on Thursday, where you can provide feedback and participate in discussions on all aspects of NCBI’s new data access options: NCBI Datasets, SRA, BLAST, and the Genome Data Viewer (GDV) — our genome browser for sequence visualization. We welcome your input!  Come and see us!

CollaborationFest (CoFest), July 31 – August 1, 2021

The ElasticBlast team will attend the BOSC CoFest following the conference. Sign up to participate on July 31 and August 1 to get an in-depth orientation and opportunity to test the capabilities of ElasticBlast on the Amazon Web Services (AWS) cloud. You do not have to register for the conference to attend the CoFest. See our post on the CoFest for more information.


Magic-BLAST version 1.6.0 is here!

Magic-BLAST version 1.6.0 is here!

We’ve just released  a new version (1.6.0) of Magic-BLAST, the BLAST-based next-gen alignment tool, with these improvements:

  • Usage reporting — you can help improve Magic-BLAST by sharing limited information about your search. The BLAST User Manual has details on the information collected, how it is used, and how to opt-out.
  • Magic BLAST can access NCBI SRA next-gen reads from the cloud when  you use the -sra or -sra_batch options.  See the Magic-BLAST cookbook for more details.
  • NCBI taxonomy IDs are reported in SAM output if they are present in the target BLAST database.
  • You can get unaligned reads reported separately from the aligned ones by using the -out_unaligned <file name> option.  You can also select the format ( SAM, tabular, or FASTA) with the -unaligned_fmt option. The default format is the same as one for the main report .

The version 1.6.0 executables are available from the NCBI FTP site.  See the release notes , the NCBI GitHub site , and the Magic-BLAST publication for more information.

NCBI at ASHG 2019: Two Data CoLabs Demonstrate How to Analyze NextGen Sequence Data and Access Genetic Variation Population Data

NCBI will be attending the American Society of Human Genetics (ASHG) 2019 in Houston Texas on Oct 15-19.

This year, we will be presenting two CoLabs – interactive sessions where you can learn about new NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG next week!

Continue reading “NCBI at ASHG 2019: Two Data CoLabs Demonstrate How to Analyze NextGen Sequence Data and Access Genetic Variation Population Data”

Magic-BLAST version 1.5.0 is here!

Magic-BLAST version 1.5.0 is here!

We’ve just released a new version of Magic-BLAST with several new, user-driven enhancements like:

  • Nanopore sequence alignment
  • Improved multithreading performance
  • Support for the new BLAST database version, BLASTDBv5, that allows you to limit your search by taxonomy
  • More reliable placements of reads

The new executables are available on the NCBI FTP site.


A new paper (PMID: 31345161), published in July 2019 by BMC Bioinformatics, presents the usage accuracy of Magic-BLAST.

Magic-BLAST aligns next generation DNA- and RNA-Seq sequencing reads. Read more about the latest version of Magic-BLAST in the release notes.

Magic-BLAST (v1.4.0), an accurate DNA and RNA-Seq aligner

What is Magic-BLAST and why are we excited about it?

Magic-BLAST is a BLAST tool, but it’s unlike any other.

It aligns next generation sequencing reads, both DNA and RNA-seq.  It implements the aligner algorithm from MAGIC [1], a trusted pipeline, but uses the well tested and supported BLAST infrastructure. We think it’s like putting two great things together, like having your favorite ice cream in your morning coffee.

We’re so excited about it that we even wrote an article that compares Magic-BLAST to a few other aligners on several data sets.

If you look at the figures in our article, we think you’ll see that Magic-BLAST excels at finding introns and processing ultra-long sequences. It also can handle high levels of mismatches as well compositionally biased DNA.  Finally, you’ll see that Magic-BLAST works in a lot of relevant situations in which current aligners won’t. If our results got your attention, here is our documentation, which includes a cookbook with a few examples.

Continue reading “Magic-BLAST (v1.4.0), an accurate DNA and RNA-Seq aligner”

5 NCBI articles in 2018 Nucleic Acids Research database issue

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

Continue reading “5 NCBI articles in 2018 Nucleic Acids Research database issue”

Magic-BLAST 1.3.0 released with new features and improvements

The newest version of Magic-BLAST (v. 1.3.0) offers improved sensitivity and faster run-times as well as a number of other new features and improvements. These include the ability to set the alignment cut-off score as a function of read length, a maximum edit distance option and optional local cacheing for SRA files. For more information on these and other improvements, see the release notes. You can download the new executables from the NCBI FTP site.

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more here.

Introducing Magic-BLAST

Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Magic-BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available on the FTP site.

Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-Seq, locating the candidate introns and adding up the score of all exons. Sequencing reads can be provided as NCBI SRA accessions, FASTA or SRA files.

Magic-BLAST implements ideas developed in the NCBI Magic pipeline using the NCBI BLAST libraries. Magic-BLAST is under active development, and we expect the next few releases to occur on a monthly basis. Read more about Magic BLAST on the FTP site.