282 Open source projects that are alternatives of or similar to psmc

Forward-time simulation in Python using fwdpp

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Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

A powerful open source data warehouse system

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

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Pinpoints the mutation favored by selection

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High-performance error correction for Illumina resequencing data

An open-source toolkit for large-scale genomic analysis

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JavaScript VisualizationTools

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cython + htslib == fast VCF and BCF processing

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An ultrafast memory-efficient short read aligner

Population assignment analysis using R

Performant Pythonic GenomicRanges

a pileup library that embraces the huge

🔬 BEDOPS: high-performance genomic feature operations

Genomics Workflows on AWS

Fast large scale matrix visualization for the web.

Biopython Jupyter Notebook tutorial to characterize a small genome

Proof-of-concept seq-to-graph mapper and graph generator

A tool for fast and accurate summarizing of variant calling format (VCF) files

Intuitive local web frontend for the BLAST bioinformatics tool

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

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A genome browser that shows long reads and complex variants better

simuG: a general-purpose genome simulator

Deep learning infrastructure for bioinformatics

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Reads simulator

Collection of scripts for bacterial genomics

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

xHLA: Fast and accurate HLA typing from short read sequence data

Viral genomics analysis pipelines

Genome-wide imputation pipeline

structural variant calling and genotyping with existing tools, but, smoothly.

A DNA Sequence Alignment/Map (SAM) library for Clojure

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Performs memory-efficient reservoir sampling on very large input files delimited by newlines