Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/nahid18/Awesome-LatchBio
A curated list of awesome Bioinformatics pipelines and software available on LatchBio
https://github.com/nahid18/Awesome-LatchBio
List: Awesome-LatchBio
awesome bioinformatics latchbio
Last synced: 3 months ago
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A curated list of awesome Bioinformatics pipelines and software available on LatchBio
- Host: GitHub
- URL: https://github.com/nahid18/Awesome-LatchBio
- Owner: nahid18
- Created: 2022-05-20T09:39:08.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2022-08-07T14:23:17.000Z (about 2 years ago)
- Last Synced: 2024-05-20T01:23:21.363Z (6 months ago)
- Topics: awesome, bioinformatics, latchbio
- Homepage: https://console.latch.bio/explore
- Size: 51.8 KB
- Stars: 12
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
Awesome Lists containing this project
- ultimate-awesome - Awesome-LatchBio - A curated list of awesome Bioinformatics pipelines and software available on LatchBio. (Other Lists / PowerShell Lists)
README
# Awesome LatchBio [](https://github.com/sindresorhus/awesome)
> Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. — [Wikipedia](https://en.wikipedia.org/wiki/Bioinformatics)
A curated list of awesome Bioinformatics pipelines and software available on [LatchBio](https://console.latch.bio/explore). Command line or programmatic tools are now with Graphical User Interface and can be run without the hassle of software installation! Please feel free to [contribute](CONTRIBUTING.md)!
## Table of Contents
- [Genome Assembly](#genome-assembly)
- [De novo](#de-novo)
- [Metrics](#metrics)
- [Circular genomes](#circular-genomes)
- [Sequence alignment](#sequence-alignment)
- [BLAST](#blast)
- [LAST](#last)
- [Multiple sequence alignment](#multiple-sequence-alignment)
- [Align](#align)
- [Trimming](#trimming)
- [Summary statistics](#summary-statistics)
- [Phylogenetics](#phylogenetics)
- [Phylogenetic inference](#phylogenetic-inference)
- [Bayesian evolutionary analysis](#bayesian-evolutionary-analysis)
- [Codon analyses](#codon-analyses)
- [Optimization](#optimization)
- [CRISPR](#crispr)
- [CRISPR locus](#crispr-locus)
- [RNA Design and Analysis](#rna-design-and-analysis)
- [NUPACK](#nupack)
- [General use](#general-use)
- [Latch console](#latch-console)
- [Contributors](#contributors)
---
### Genome Assembly
#### De novo
- **[shasta](https://github.com/chanzuckerberg/shasta)**
**Shasta** | [latch source code](https://github.com/nahid18/shasta) | [paper-2020](https://pubmed.ncbi.nlm.nih.gov/32686750) | [documentation](https://chanzuckerberg.github.io/shasta)
- Rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input.
#### Metrics
- **[BioKIT genome assembly metrics](https://jlsteenwyk.com/BioKIT/)**
**wf.genome_assembly_metrics_biokit** | [paper-2022](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183) | [documentation](https://jlsteenwyk.com/BioKIT/)
- Calculate diverse summary statistics for a genome assembly using [BioKIT](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183)
#### Circular genomes
- **[Circlator](https://console.latch.bio/explore/60347/info)**
[github repo](https://github.com/matteobolner/latch_workflows) | [paper-2015](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0)
- Circlator is a post-assembly improvement toolkit for producing correctly represented circular DNA structures.
### Sequence alignment
#### BLAST
- **makeblastdb**
| [Latch Workflow](https://console.latch.bio/explore/65929/info) | [Source Code](https://github.com/matteobolner/latch_workflows/tree/master/makeblastdb) | [Documentation](https://www.ncbi.nlm.nih.gov/books/NBK279670/)
- Produce BLAST databases from FASTA files
- **blast**
| Coming soon
- Align biological sequences against other sequences or a database indexed with makeblastdb
#### LAST
- **lastdb**
| [Latch Workflow](https://console.latch.bio/explore/64352/info) | [Source Code](https://github.com/matteobolner/latch_workflows/tree/master/lastdb) | [Related Papers](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-papers.rst) | [Documentation](https://gitlab.com/mcfrith/last/-/tree/main)
- Prepare sequences for subsequent comparison and alignment using lastal
- **lastal**
| [Latch Workflow](https://console.latch.bio/explore/65242/info) | [Source Code](https://github.com/matteobolner/latch_workflows/tree/master/lastal) | [Related Papers](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-papers.rst) | [Documentation](https://gitlab.com/mcfrith/last/-/tree/main)
- Find local alignments between query sequences, and reference sequences that have been prepared using lastdb.
### Multiple sequence alignment
#### Align
- **[MAFFT](https://mafft.cbrc.jp/alignment/software/)**
**wf.align_sequences_mafft** | [paper-2013](https://academic.oup.com/mbe/article/30/4/772/1073398) | [documentation](https://mafft.cbrc.jp/alignment/software/))
- Multiple sequence alignment program.
- **[CIAlign](https://github.com/KatyBrown/CIAlign.git)**
**wf.CIAlign** | [Paper](https://peerj.com/articles/12983/) | [Documentation](https://github.com/GeOdette/clalign.git)
- Clean, visualise, and interpret multiple sequence alignment.
#### Trimming
- **[ClipKIT](https://github.com/JLSteenwyk/ClipKIT)**
**wf.clipkit** | [paper-2020](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007) | [documentation](https://jlsteenwyk.com/ClipKIT/)
- Multiple sequence alignment trimming for accurate phylogenomic inference.
- **[CIAlign](https://github.com/KatyBrown/CIAlign.git)
**wf.CIAlign** | [Latch source code](https://github.com/GeOdette/clalign.git) | [Documentation](https://github.com/GeOdette/clalign.git)
- Clean, visualise, and interpret the multiple sequence alignment
#### Summary statistics
- **[BioKIT alignment_summary_statistics](https://jlsteenwyk.com/BioKIT/)**
**wf.alignment_summary_statistics** | [paper-2022](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183) | [documentation](https://jlsteenwyk.com/BioKIT/)
- Calculate diverse summary statistics for a multiple sequence alignment using [BioKIT](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183)
### Phylogenetics
#### Phylogenetic inference
- **[IQ-TREE2](http://www.iqtree.org/doc/)**
**wf.infer_phylogeny** | [paper-2020](https://doi.org/10.1093/molbev/msaa015) | [documentation](http://www.iqtree.org/doc/)
- Efficient software for phylogenomic inference.
#### Bayesian evolutionary analysis
- **BEAST**
| [Latch Workflow](https://console.latch.bio/explore/62992/info) | [Source Code](https://github.com/matteobolner/latch_workflows/tree/master/beast) | [Related Papers](https://doi.org/10.1093/ve/vey016) | [Documentation](https://beast.community/)
- Bayesian analysis of molecular sequences using Monte Carlo Markov Chain
### Codon analyses
#### Optimization
- **[BioKIT gRSCU](https://jlsteenwyk.com/BioKIT/)**
**wf.codon_optimization_biokit** | [paper-2022](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183) | [documentation](https://jlsteenwyk.com/BioKIT/)
- Estimate codon optimization using [BioKIT](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183)
### CRISPR
#### CRISPR locus
- **[CRISPRbuilderTB](https://github.com/GeOdette/crisptb.git)**
**wf.CRISPRbuilderTB** | [Paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008500) | [documentation](https://github.com/GeOdette/crisptb.git)
- Reconstruct Mycobacterium tuberculosis CRISPR-Cas loci from short reads using [CRISPRbuilder-TB](https://github.com/cguyeux/CRISPRbuilder-TB.git)
### RNA Design and Analysis
#### NUPACK
- **NUPACK Loop and Stack Energies**
| [Latch Workflow](https://console.latch.bio/explore/62122/info) | [Source Code](https://github.com/beliveau-lab/NUPACK) | [Related Papers](https://docs.nupack.org/#citation) | [Documentation](https://docs.nupack.org/model/)
- Analyse loop free energy and stacking state free energies for single and multiloop structures using NUPACK
- **NUPACK - Utilities**
| [Latch Workflow](https://console.latch.bio/explore/62158/info) | [Source Code](https://github.com/beliveau-lab/NUPACK) | [Related Papers](https://docs.nupack.org/#citation) | [Documentation](https://docs.nupack.org/utilities/)
- Structural analysis using [NUPACK Utilities](https://docs.nupack.org/utilities/) for a complex formed between two nucleotide strands
### General use
#### Latch console
- **Downloader** | [Latch Workflow](https://console.latch.bio/explore/61426/info) | [Source Code](https://github.com/matteobolner/latch_workflows/tree/master/downloader)
- Download files directly in the Latch Console
### Contributors
