<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43926?offset=220 https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator Wed, 08 Mar 2023 01:39:33 -0600 https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator <![CDATA[ALE: Assembly Likelihood Estimator]]> Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly.  Depending on your genome size you may want to convert the .wig files to the BigWig format.

Address of the bookmark: https://github.com/sc932/ALE

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly Sat, 08 Jun 2024 16:15:25 -0500 https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly <![CDATA[MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly]]> The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

]]> Abhi https://bioinformaticsonline.com/news/view/40589/new-layout-for-blast-ftp-database-site Tue, 21 Jan 2020 11:57:11 -0600 https://bioinformaticsonline.com/news/view/40589/new-layout-for-blast-ftp-database-site <![CDATA[New Layout for BLAST ftp Database Site]]> As announced previously, the new default database version for BLAST+ is dbV5.  To complete this transition, the ftp database site will be updated to support this change.  We expect this change to happen around February 4th, please adjust your scripts or procedures accordingly.

Here is a list of what is changing:

  1. All databases at the root level will be dbV5.
  2. The dbV5 file naming,  “_v5” will be removed. Databases with  no “_vX” descriptor will be dbV5.
  3. dbV4 tarballs will be renamed with "_v4", files included in tarball will not be renamed.
  4. dbV4 databases will be moved to a v4 subdirectory.
  5. As of 1/13/20 the Cloud directory will be frozen with no more new entries.
  6. The will be no more updates to dbV4 databases.
  7. The FASTA directory will contain nr, nt, swissprot, and pdbaa files.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

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