spades
seqkit
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| spades | seqkit | |
|---|---|---|
| 4 | 3 | |
| 660 | 1,202 | |
| 2.6% | - | |
| 9.3 | 8.5 | |
| 11 days ago | 21 days ago | |
| C++ | Go | |
| 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
seqkit
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A look at the Mojo language for bioinformatics
I've been thinking to learn Rust for these use cases, but always get frustrated with the complexity.
I find Go is a great middle-ground though! And now there starts to be a few more bio-related tools and toolkits out there, including:
- https://github.com/vertgenlab/gonomics
- https://github.com/biogo/biogo
- https://github.com/shenwei356/bio
... except from there being some really popular bio tools written in Go, like:
- https://github.com/shenwei356/seqkit
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Help with understanding awk code
You could also check out tools specialized for FASTA processing like https://github.com/shenwei356/seqkit and https://github.com/lh3/seqtk
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What are some good examples of well-engineered bioinformatics pipelines?
Seqkit - thoroughly maintained with extensive tutorials and benchmarking info - https://github.com/shenwei356/seqkit
What are some alternatives?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
seqtk - Toolkit for processing sequences in FASTA/Q formats
mag - Assembly and binning of metagenomes
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)
rush - A cross-platform command-line tool for executing jobs in parallel
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.
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files