{"id":14111480,"url":"https://github.com/nahid18/Awesome-LatchBio","last_synced_at":"2025-08-01T12:32:53.955Z","repository":{"id":39705747,"uuid":"494405198","full_name":"nahid18/Awesome-LatchBio","owner":"nahid18","description":"A curated list of awesome Bioinformatics pipelines and software available on LatchBio","archived":false,"fork":false,"pushed_at":"2022-08-07T14:23:17.000Z","size":53,"stargazers_count":12,"open_issues_count":0,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-05-20T01:23:21.363Z","etag":null,"topics":["awesome","bioinformatics","latchbio"],"latest_commit_sha":null,"homepage":"https://console.latch.bio/explore","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nahid18.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-05-20T09:39:08.000Z","updated_at":"2023-12-26T13:35:31.000Z","dependencies_parsed_at":"2022-08-28T11:23:10.962Z","dependency_job_id":null,"html_url":"https://github.com/nahid18/Awesome-LatchBio","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nahid18%2FAwesome-LatchBio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nahid18%2FAwesome-LatchBio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nahid18%2FAwesome-LatchBio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nahid18%2FAwesome-LatchBio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nahid18","download_url":"https://codeload.github.com/nahid18/Awesome-LatchBio/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228375964,"owners_count":17910313,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["awesome","bioinformatics","latchbio"],"created_at":"2024-08-14T10:03:19.350Z","updated_at":"2024-12-05T21:31:15.831Z","avatar_url":"https://github.com/nahid18.png","language":null,"funding_links":[],"categories":["Other Lists"],"sub_categories":["TeX Lists"],"readme":"# Awesome LatchBio [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome)\n\n\u003e Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. — [Wikipedia](https://en.wikipedia.org/wiki/Bioinformatics)\n\nA 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)!\n\n\u003c!-- START doctoc generated TOC please keep comment here to allow auto update --\u003e\n\u003c!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE --\u003e\n## Table of Contents\n\n- [Genome Assembly](#genome-assembly)\n  - [De novo](#de-novo)\n  - [Metrics](#metrics)\n  - [Circular genomes](#circular-genomes)\n- [Sequence alignment](#sequence-alignment)\n  - [BLAST](#blast)\n  - [LAST](#last)\n- [Multiple sequence alignment](#multiple-sequence-alignment)\n  - [Align](#align)\n  - [Trimming](#trimming)\n  - [Summary statistics](#summary-statistics)\n- [Phylogenetics](#phylogenetics)\n  - [Phylogenetic inference](#phylogenetic-inference)\n  - [Bayesian evolutionary analysis](#bayesian-evolutionary-analysis)\n- [Codon analyses](#codon-analyses)\n  - [Optimization](#optimization)\n- [CRISPR](#crispr)\n  - [CRISPR locus](#crispr-locus)\n- [RNA Design and Analysis](#rna-design-and-analysis)\n  - [NUPACK](#nupack)\n- [General use](#general-use)\n  - [Latch console](#latch-console)\n- [Contributors](#contributors)\n\n\u003c!-- END doctoc generated TOC please keep comment here to allow auto update --\u003e\n\n---\n\n### Genome Assembly\n\n#### De novo\n\n- **[shasta](https://github.com/chanzuckerberg/shasta)** \n  \u003cbr/\u003e\n  **Shasta** | [latch source code](https://github.com/nahid18/shasta) | [paper-2020](https://pubmed.ncbi.nlm.nih.gov/32686750) | [documentation](https://chanzuckerberg.github.io/shasta)\n  - Rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input.\n\n#### Metrics\n- **[BioKIT genome assembly metrics](https://jlsteenwyk.com/BioKIT/)**\n  \u003cbr/\u003e\n  **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/)\n  - Calculate diverse summary statistics for a genome assembly using [BioKIT](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183) \n  \n#### Circular genomes\n- **[Circlator](https://console.latch.bio/explore/60347/info)**\n  \u003cbr/\u003e\n  [github repo](https://github.com/matteobolner/latch_workflows) | [paper-2015](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0)\n   - Circlator is a post-assembly improvement toolkit for producing correctly represented circular DNA structures.\n\n### Sequence alignment\n\n#### BLAST\n- **makeblastdb**\n  | [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/)\n  - Produce BLAST databases from FASTA files\n- **blast**\n  | Coming soon\n  - Align biological sequences against other sequences or a database indexed with makeblastdb\n\n#### LAST\n- **lastdb**\n  | [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)\n  - Prepare sequences for subsequent comparison and alignment using lastal\n- **lastal**\n  | [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)\n  - Find local alignments between query sequences, and reference sequences that have been prepared using lastdb.\n\n### Multiple sequence alignment\n\n#### Align\n- **[MAFFT](https://mafft.cbrc.jp/alignment/software/)**\n  \u003cbr/\u003e\n  **wf.align_sequences_mafft** | [paper-2013](https://academic.oup.com/mbe/article/30/4/772/1073398) | [documentation](https://mafft.cbrc.jp/alignment/software/))\n  - Multiple sequence alignment program.\n\n- **[CIAlign](https://github.com/KatyBrown/CIAlign.git)**\n  \u003cbr/\u003e\n  **wf.CIAlign** | [Paper](https://peerj.com/articles/12983/) | [Documentation](https://github.com/GeOdette/clalign.git)\n  - Clean, visualise, and interpret multiple sequence alignment.\n\n#### Trimming\n- **[ClipKIT](https://github.com/JLSteenwyk/ClipKIT)** \n  \u003cbr/\u003e\n  **wf.clipkit** | [paper-2020](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007) | [documentation](https://jlsteenwyk.com/ClipKIT/)\n  - Multiple sequence alignment trimming for accurate phylogenomic inference.\n\n\n- **[CIAlign](https://github.com/KatyBrown/CIAlign.git)\n  \u003cbr/\u003e\n  **wf.CIAlign** | [Latch source code](https://github.com/GeOdette/clalign.git) | [Documentation](https://github.com/GeOdette/clalign.git)\n  - Clean, visualise, and interpret the multiple sequence alignment\n\n#### Summary statistics\n- **[BioKIT alignment_summary_statistics](https://jlsteenwyk.com/BioKIT/)**\n  \u003cbr/\u003e\n  **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/)\n  - 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)\n\n### Phylogenetics\n\n#### Phylogenetic inference\n- **[IQ-TREE2](http://www.iqtree.org/doc/)** \n  \u003cbr/\u003e\n  **wf.infer_phylogeny** | [paper-2020](https://doi.org/10.1093/molbev/msaa015) | [documentation](http://www.iqtree.org/doc/)\n  - Efficient software for phylogenomic inference.\n#### Bayesian evolutionary analysis\n- **BEAST**\n  | [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/)\n  - Bayesian analysis of molecular sequences using Monte Carlo Markov Chain\n\n\n### Codon analyses\n\n#### Optimization\n- **[BioKIT gRSCU](https://jlsteenwyk.com/BioKIT/)** \n  \u003cbr/\u003e\n  **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/)\n  - Estimate codon optimization using [BioKIT](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac079/6583183)\n\n### CRISPR\n#### CRISPR locus\n- **[CRISPRbuilderTB](https://github.com/GeOdette/crisptb.git)**\n  \u003cbr/\u003e\n  **wf.CRISPRbuilderTB** | [Paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008500) | [documentation](https://github.com/GeOdette/crisptb.git)\n  - Reconstruct Mycobacterium tuberculosis CRISPR-Cas loci from short reads using [CRISPRbuilder-TB](https://github.com/cguyeux/CRISPRbuilder-TB.git)\n\n### RNA Design and Analysis\n#### NUPACK\n- **NUPACK Loop and Stack Energies**\n  | [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/)\n  - Analyse loop free energy and stacking state free energies for single and multiloop structures using NUPACK\n \n- **NUPACK - Utilities**\n  | [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/)\n  - Structural analysis using [NUPACK Utilities](https://docs.nupack.org/utilities/) for a complex formed between two nucleotide strands\n\n### General use\n#### Latch console\n- **Downloader** | [Latch Workflow](https://console.latch.bio/explore/61426/info) | [Source Code](https://github.com/matteobolner/latch_workflows/tree/master/downloader) \n  - Download files directly in the Latch Console\n\n### Contributors\n![Your Repository's Stats](https://contrib.rocks/image?repo=nahid18/Awesome-LatchBio)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnahid18%2FAwesome-LatchBio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnahid18%2FAwesome-LatchBio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnahid18%2FAwesome-LatchBio/lists"}