| masurca | mag | |
|---|---|---|
| 1 | 2 | |
| 229 | 182 | |
| - | 1.6% | |
| 3.5 | 9.4 | |
| 2 months ago | 11 days ago | |
| M4 | Nextflow | |
| GNU General Public License v3.0 only | MIT License |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
masurca
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Nanopore long read assembly help!
Hybrid assembly: https://github.com/alekseyzimin/masurca
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?
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
SqueezeMeta - A complete pipeline for metagenomic analysis
bioinformatics - Bioinformatic algorithms for the UCLA Bioinformatics Specialization
atlas - Manage your database schema as code
Trycycler - A tool for generating consensus long-read assemblies for bacterial genomes
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
spades - SPAdes Genome Assembler
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
nextflow - A DSL for data-driven computational pipelines
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing