Genomics

Links
​Seq - Programming language for high-performance computational genomics. (Web) (HN)
​Open sourcing bioinstruments (2019) (HN)
​goleft - Collection of bioinformatics tools distributed under MIT license in a single static binary.
​When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data (2019)​
​Handbook of Statistical Genomics (2019)​
​Nature Reviews Genetics - Monthly review journal in genetics and covers the full breadth of modern genetics.
​Bioinformatics and Functional Genomics 3rd Edition by Jonathan Pevsner​
​Nucleus - Python and C++ code for reading and writing genomics data.
​Statistical Population Genomics​
​Genome Informatics 2019 Lightning Talk: A. Sina Booeshaghi​
​10x Genomics (Code)
​Neher Lab - Pathogen evolution, genomics, and biophysics lab in Switzerland.
​BEDOPS - High-performance genomic feature operations.
​Introduction to Genetics and Evolution​
​Open Targets - Partnership that uses human genetics and genomics data for systematic drug target identification and prioritisation.
​Next-Gen Sequence Analysis Workshop (2019)​
​Korkin Lab​
​Varlociraptor - Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
​genetools - Single-cell analysis recipes. (Code)
​Learn Genetics (HN)
​fgsea - Fast Gene Set Enrichment Analysis.
​Awesome Genome Visualization​
​Computational Genomics Class Playlist at San Diego State University​
​Computational Genomics Manual (Code)
​A Theory of Natural Universal Computation Through RNA (2020) (Tweet)
​Hail - Open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data. (References) (Web)
​gnomAD - Genome aggregation database.
​gnomad_methods - Hail helper functions for the gnomAD project and Translational Genomics Group.
​We can now edit the human genome – how far should we go? (HN)
​Scientific Background: A tool for genome editing (2020)​
​Introduction to Social Science Genetics (2020)​
​gplearn - Implements Genetic Programming in Python, with a scikit-learn inspired and compatible API.
​Genetic List - Browsable genetic marker lists.
​Cutevariant - Standalone and free application to explore genetics variations from VCF file.
​A hypothesis is a liability (2020)​
​Awesome Imaging Genetics​
​There is little chance CRISPR will ever be widely used to directly treat disease (2020) (HN)
​misha - Genomic data analysis suite.
​MetaCell R - Single-cell mRNA Analysis.
​nf-core/eager - Bioinformatics best-practice analysis pipeline for NGS sequencing based ancient DNA (aDNA) data analysis.
​GenomicSQLite - Genomics Extension for SQLite.
​gfabase - Command-line utility for random-access storage of Graphical Fragment Assembly (GFA) data.
​GenomeSpy - Genome visualization tool with a grammar of graphics and WebGL-powered fluid interactions. (Code)
​Decoding the Language of Genomes (2020) (HN)
​GREIN - GEO RNA-seq Experiments Interactive Navigator. (Code)
​FUMA: Functional mapping and annotation of genetic associations (Code)
​GenePattern Notebook - Platform for integrating genomic analysis with Jupyter Notebooks.
​SCDE - R package for analyzing single-cell RNA-seq data.
​Human Genome Idiogram Vector Art Library - Contains image files for each of the 24 primary human chromosomes, as well as one for the entire genome lined up.
​RNA Memory Hypothesis (2021) (HN)
​ELI5 Epigenetics​
​Bioconductor - Provides tools for the analysis and comprehension of high-throughput genomic data. (GitHub)
​Orchestrating Single-Cell Analysis with Bioconductor (Code)
​Awesome CRISPR - List of software/websites/databases/papers for genome engineering.
​Genomics Workflows on AWS (Web)
​Pyne Lab - Single molecule biophysics of DNA interactions.
​Nextclade - Viral genome alignment, clade assignment, mutation calling, and quality checks. (Code)
​Shooting out the messenger—mRNA and how the pandemic advanced biotechnologies (2021) (Tweet)
​Cirrocumulus for Single-Cell Data Visualization (Code)
​On detecting gene-gene interactions (2020)​
​An on-off switch for gene editing (2021)​
​Scientists Catch Jumping Genes Rewiring Genomes (2021) (HN)
​regenie - C++ program for whole genome regression modelling of large genome-wide association studies.
​Edinburgh Genome Foundry (GitHub)
​Cultural Evolution of Genetic Heritability (2021) (Tweet)
​Pachter Lab - Develops computational and experimental methods for genomics. (GitHub)
​The complete sequence of a human genome (2021) (Reddit)
​perbase - Per-base per-nucleotide depth analysis.
​Computational genomics resources​
​Seq-N-Slide - Sequencing data analysis pipelines. (Docs)
​Genomics Reddit​
​How to sequence your genome at home (2021) (HN)
​Ask HN: What's an interesting DIY genetic engineering project? (2021)​
​Illumina - Sequencing and array-based solutions for genetic research.
​Wochenende - Whole Genome/Metagenome Sequencing Alignment Pipeline.
​Using a Quadruplet Codon to Expand the Genetic Code of an Animal (2021)​
​PingPong - Comparative genome analysis using sample-specific string detectionin accurate long reads.
​RNA demethylation increases rice and potato yields 50% (2021) (HN)
​Amazon Genomics CLI (HN) (Code)
​The Specious Art of Single-Cell Genomics (2021) (Tweet) (Tweet)
​IGV: Integrative Genomics Viewer - Fast, efficient, scalable visualization tool for genomics data and annotations. (Code)
​Oxford Nanopore Technologies - Nanopores for single molecule (DNA/RNA, protein) analysis using the MinION, GridION and PromethION systems. (GitHub)
​Medaka - Tool to create consensus sequences and variant calls from nanopore sequencing data.
​alignment-nf - Whole Exome/Whole Genome Sequencing alignment pipeline.
​Stanford researchers develop an engineered 'mini' CRISPR genome editing system (2021) (HN)
​PiGx - Pipelines in genomics. (Web)
​snps - Tools for reading, writing, merging, and remapping SNPs.
​Sano Genetics - Upload DNA data to explore personal DNA reports on health, traits and genetic conditions.
​GenomePrep - To preprocess, quality control and prepare consumer DTC genomes for research. (Web)
​scikit-allel - Python package for exploring and analyzing genetic variation data.
​Centre for Genomics and Global Health (GitHub)
​pysamstats - Fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
​Local PCA - Methods for examining PCA locally along the genome.
​List of gene lists for genomic analyses​
​MacArthur Lab - Extracting useful information from large genomic datasets. (GitHub)
​Directed evolution of rRNA improves translation kinetics and recombinant protein yield (2021) (Tweet)
​classify-genomes - Classify a genome sequence according to the mOTUs/specI taxonomy.
​mOTU profiler - Computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
​Unicycler - Hybrid assembly pipeline for bacterial genomes.
​Trycycler - Tool for generating consensus long-read assemblies for bacterial genomes.
​Badread - Read simulator that can imitate many types of read problems.
​Polypolish - Short-read polishing tool for long-read assemblies.
​Holt Lab - Microbial genomics.
​Prodigal - Prodigal Gene Prediction Software.
​Predicting gene expression with AI | DeepMind (2021) (Code)
​Clonal dominance in excitable cell networks (2021)​
​'Useless Specks of Dust' Turn Out to Be Building Blocks of All Vertebrate Genome (2021) (HN)
​RNA-responsive elements for eukaryotic translational control (2021)​
​souporcell - Clustering scRNAseq by genotypes.
​Vireo - Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.
​Naturally occurring modified ribonucleosides (2020)​
​microPIPE - Pipeline for high-quality bacterial genome construction using ONT sequencing.
​Genomic Medicine and Statistics DPhil Programme​
​RNA Takes Over (HN)
​Dense Depth Data Dump (D4) - Format and tool suite provide an alternative to BigWig for fast analysis and compact storage of quantitative genomics datasets.
​bedtools - Swiss army knife for genome arithmetic.
​GEMINI - Integrative exploration of genetic variation and genome annotations.
​Quinlan Lab - Combine computational and genomic techniques to explore genome biology and the genetic basis of traits.
​vg - Tools for working with genome variation graphs.
​seqwish - Alignment to variation graph inducer.
​pggb - Pangenome graph construction pipeline renders a collection of sequences into a pangenome graph.
​Alen - Command-like program to view DNA or protein alignments in FASTA formats.
​gffutils - Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations.
​The origins and functional effects of postzygotic mutations throughout the human lifespan (2021)​
​In genetic programming, does introducing changes (e.g., mutations) at lower levels of a genome tree generally makes for better or worse outcomes than making changes at a higher level in the tree?​
​biowasm - WebAssembly modules for genomics.
​Aioli - Framework for building fast genomics web tools with WebAssembly and WebWorkers.
​42basepairs - Better way to explore your genomics data.
​A catalogue of 1,167 genomes from the human gut archaeome (2021)​
Evolution
DNA
Last modified 18d ago
Copy link