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| spades | mag | |
|---|---|---|
| 4 | 2 | |
| 664 | 182 | |
| 3.2% | 4.4% | |
| 9.3 | 9.4 | |
| about 8 hours ago | 6 days ago | |
| C++ | Nextflow | |
| GNU General Public License v3.0 or later | MIT License |
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spades
- my friend showed me his code, thees are all functions
- What are some good examples of well-engineered bioinformatics pipelines?
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Genome analysis cost
If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.
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Is it possible to assemble a complete bacterial genome using short reads?
MetaSpades has a cool option to hybrid reform contigs using short and long reads so you could pair short read data and long read data (PacBio/ONT) to get the best hybrid assembly with high throughput and long reference reads for resolving the reassembling. https://github.com/ablab/spades
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?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
SqueezeMeta - A complete pipeline for metagenomic analysis
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
atlas - Manage your database schema as code
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
nextflow - A DSL for data-driven computational pipelines
sage - Proteomics search & quantification so fast that it feels like magic
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