aviary
masurca
| aviary | masurca | |
|---|---|---|
| 3 | 1 | |
| 68 | 230 | |
| - | - | |
| 9.0 | 3.5 | |
| 8 days ago | 3 months ago | |
| Python | M4 | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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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
masurca
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Nanopore long read assembly help!
Hybrid assembly: https://github.com/alekseyzimin/masurca
What are some alternatives?
metaWRAP - MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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
bioinformatics - Bioinformatic algorithms for the UCLA Bioinformatics Specialization
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
mag - Assembly and binning of metagenomes
Trycycler - A tool for generating consensus long-read assemblies for bacterial genomes
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
drep - Rapid comparison and dereplication of genomes