<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43353?offset=70 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

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/37618/snakemake%E2%80%94a-scalable-bioinformatics-workflow-engine Sun, 02 Sep 2018 16:32:42 -0500 https://bioinformaticsonline.com/bookmarks/view/37618/snakemake%E2%80%94a-scalable-bioinformatics-workflow-engine <![CDATA[Snakemake—a scalable bioinformatics workflow engine]]> Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. 

Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data Thu, 30 May 2019 04:06:13 -0500 https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data <![CDATA[snakepipes: A toolkit based on snakemake and python for analysis of NGS data]]> snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

  • DNA-mapping*
  • ChIP-seq*
  • RNA-seq*
  • ATAC-seq*
  • scRNA-seq
  • Hi-C
  • Whole Genome Bisulfite Seq/WGBS

(*Also available in "allele-specific" mode)

snakePipes can be installed via conda :

'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

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