<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34246?offset=320 https://bioinformaticsonline.com/bookmarks/view/39370/multiphate-bioinformatics-pipeline-for-functional-annotation-of-phage-isolates Thu, 16 May 2019 00:17:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39370/multiphate-bioinformatics-pipeline-for-functional-annotation-of-phage-isolates <![CDATA[multiPhATE: bioinformatics pipeline for functional annotation of phage isolates]]> multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-, and phage-centric databases. 

 

Address of the bookmark: https://github.com/carolzhou/multiPhATE

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/41030/slr-superscaffolder-a-scaffold-assemble-pipeline-for-stlfr-reads Fri, 14 Feb 2020 14:23:30 -0600 https://bioinformaticsonline.com/bookmarks/view/41030/slr-superscaffolder-a-scaffold-assemble-pipeline-for-stlfr-reads <![CDATA[SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.]]> This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.

Here is an illustration of this pipeline:

 image

Address of the bookmark: https://github.com/BGI-Qingdao/SLR-superscaffolder

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins Mon, 17 Aug 2020 05:25:10 -0500 https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins <![CDATA[SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins]]> SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

  1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
  2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
  3. Includes binning and bin checking, for retrieving individual genomes
  4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
  5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
  6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43353/judi-just-do-it Mon, 06 Sep 2021 02:44:35 -0500 https://bioinformaticsonline.com/bookmarks/view/43353/judi-just-do-it <![CDATA[JUDI: Just Do It]]> judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings.

https://github.com/ncbi/JUDI

Address of the bookmark: https://github.com/ncbi/JUDI

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44595/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins Sat, 06 Jul 2024 04:29:16 -0500 https://bioinformaticsonline.com/bookmarks/view/44595/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins <![CDATA[SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins]]> SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

  1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
  2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
  3. Includes binning and bin checking, for retrieving individual genomes
  4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
  5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
  6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

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