spades
gatk4-genome-processing-pipeline-azure
| spades | gatk4-genome-processing-pipeline-azure | |
|---|---|---|
| 4 | 4 | |
| 664 | 7 | |
| 1.7% | - | |
| 9.3 | 0.0 | |
| 4 days ago | about 2 months ago | |
| C++ | wdl | |
| GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" 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
gatk4-genome-processing-pipeline-azure
- What are some good examples of well-engineered bioinformatics pipelines?
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Do you know how to get CNVs out of WES data sorted.bam files? (Free)
The GATK suite is pretty standard for calling germline mutations. Somatic mutation calling is a lot newer/trickier, so I'm just going to link to the GDC's practices.
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Best way to document tool?
This pre-processing pipeline from Microsoft (adapted from the Broad Institute/GATK) is pretty well-documented - at least in my opinion - with input requirements, expected outputs, software requirements, etc.
What are some alternatives?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
mag - Assembly and binning of metagenomes
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
sage - Proteomics search & quantification so fast that it feels like magic
bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
veba - A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.