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Name: Patrick Reilly
Type: User
Bio: Postdoc working in human evolutionary genomics, used to work in population genomics of Drosophila and Lepidoptera, unreasonably fond of awk
Twitter: LePatoptera
Name: Patrick Reilly
Type: User
Bio: Postdoc working in human evolutionary genomics, used to work in population genomics of Drosophila and Lepidoptera, unreasonably fond of awk
Twitter: LePatoptera
Annotated Genome Optimization Using Transcriptome Information
Program for analysing NGS data.
Method to estimate the age and intensity of recent bottlenecks/founder events, using genotype data and a recombination map.
Application for the visualisation of draft genome assemblies and general QC
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
Program to transpose large CSV files
Deduplicate alignments in BAMs merged from adjacent (possibly overlapping) regions. These duplicated alignments are generally artifacts of a scatter-gather process. (My first Rust project)
Scripts used for processing and analyses of PacBio genomes (and popgen samples mapped to these references) from the Drosophila yakuba clade (D. santomea, D. teissieri, and D. yakuba)
Scripts used for analyses of inversions in Drosophila yakuba
A basic Python-based EGA download client
Nextflow pipeline for generating per-sample gVCFs from sequencing read FASTQs (initially implemented for human data following slight modifications of the GATK Best Practices)
finshingTool
Nextflow pipeline for generating multi-sample VQSR- and dbSNP-annotated VCFs from per-sample gVCFs generated by fastq_to_gvcf.nf. Also contains a pipeline for preparing dbSNP and archaic hominin VCFs for usage with hs37d5 modern human VCFs.
Simple evaluation of haplotypes reconstructed from simulated reads
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
Scripts used for pre- and post-processing of various human population genomics analyses
A swift, versatile phylogenomic and high-throughput sequencing simulator
Basic QC pipeline for low-depth Illumina data, mainly intended for human data and used for the PIBv1 dataset
lumpy: a general probabilistic framework for structural variant discovery
Multiplexed Shotgun Genotyping
Updated version of non-competitive Allele-Specific Expression method originally designed by Maria Gutin
Illumina data parsing scripts (for use when i5 and/or i7 index reads are provided as separate synchronized FASTQs)
Phase multi-sample VCF using read-informed statistical phasing (i.e. WhatsHap for read-backed phasing, fed into SHAPEIT4 statistical phasing without reference panel) along with evaluation of phasing quality and error rates using trios.
Processing and analysis pipelines for the manuscript titled "Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania"
Parallelized pipeline for alignment, variant calling, and generation of pseudoreference FASTAs from Illumina data (DNA- or RNAseq)
Collection of arbitrary (perhaps useful) programs and scripts, and occasional one-liners
Software for estimating genome-wide genealogies for thousands of samples
A pipeline to call structural variants from genome alignment
Variant Calling Simulation pipeline for diverged and polymorphic genomes
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.