aviary
mag
aviary | mag | |
---|---|---|
3 | 2 | |
68 | 182 | |
- | 1.6% | |
9.0 | 9.4 | |
8 days ago | 5 days ago | |
Python | Nextflow | |
GNU General Public License v3.0 only | MIT License |
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aviary
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what would you choose to detect specific genes in metagenomics data
Aviary is a good binning pipeline (there are others available), though perhaps more geared towards prokaryotes.
- Why bother reconstructing MAGs ?
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question about analysis of metagenome assembled genomes
Have a look at this especially the workflow figure https://github.com/rhysnewell/aviary
mag
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How do you use Termux?
So, I'm a bioinformatician, and currently I am extending my company's data processing pipeline which takes metagenomic sequencing data and performs a number of downstream analyses on it, the results of which are then provided to our customers. Here is an example of such a data processing pipeline: it's a script which orchestrates the execution of a number of tools to get the desired end result. Each of the green bubbles in the flowchart represents a single program which needs to be called specific settings and with data provided to it either by me (as the pipeline input) or from outputs of previous steps in the pipeline.
- Is it possible to assemble a complete bacterial genome using short reads?
What are some alternatives?
metaWRAP - MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
SqueezeMeta - A complete pipeline for metagenomic analysis
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
atlas - Manage your database schema as code
masurca
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
spades - SPAdes Genome Assembler
nextflow - A DSL for data-driven computational pipelines
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Atlas - 🚀 An open and lightweight modification to Windows, designed to optimize performance, privacy and security.