ant-design-pro - 👨🏻‍💻👩🏻‍💻 Use Ant Design like a Pro!

•    Javascript

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An out-of-box UI solution for enterprise applications as a React boilerplate. More instructions at documentation.

antd react redux css design desktop enterprise boilerplate admin admin-dashboard umi firebase

umi - 🌋 Pluggable enterprise-level react application framework.

•    Javascript

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🌋 Pluggable enterprise-level react application framework. Please consider following this project's author, sorrycc, and consider starring the project to show your ❤️ and support.

umi react-framework umijs

fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

•    C++

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A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. By default, the HTML report is saved to fastp.html (can be specified with -h option), and the JSON report is saved to fastp.json (can be specified with -j option).

fastq qc preprocessing filtering adapter overlap quality trimming splitting quality-control filter ngs bioinformatics overlapping error umi sequencing illumina polyg duplication

dropSeqPipe - A SingleCell RNASeq pre-processing pipeline built on snakemake

•    R

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This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab. It allows to go from raw data of your Single Cell RNA seq experiment until the final count matrix with QC plots along the way. This is the tool we use in our lab to improve our wetlab protocol as well as provide an easy framework to reproduce and compare different experiments with different parameters.

drop-seq snakemake pipeline dropseq yaml star picard reference-genome umi scrbseq scrb-seq multiqc conda plot dropseqtools

umi-examples - examples for umi.js

•    Javascript

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examples for umi.js

sample umi datahub

umi-plugin-locale - A umi plugin for provide internationalization function.

•    Javascript

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Umi plugin for i18n, based on react-intl. This is the 1.0 repo, it is for umi 1.0. If you are look for 2.0, visit: https://github.com/umijs/umi/tree/master/packages/umi-plugin-locale .

umi

fastq_utils - Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification

•    C

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Set of Linux utilities to validate and manipulate fastq files. It also includes a set of programs to preprocess barcodes (namely UMIs, cells and samples), add the barcodes as tags in BAM files and count UMIs. samtools (version 0.1.19) and zlib (http://zlib.net) version 1.2.11 or latest are required to compile fastq_utils. The install_deps.sh script in the toplevel folder tries to download and compile the dependencies. The bam_annotate.sh script requires samtools (version 1.5 or higher).

sequencing fastq validation ngs high-throughput-sequencing fastq-filterpair umi single-cell drop-seq 10x umi-count digital-gene-expression dge barcodes scrna-seq

mageri - MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

•    Java

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Molecular tagging approach has revolutionized the field of high depth genome re-sequencing by allowing detection of ultra-rare mutations. This pipeline aims at filling the gap in software for analysis of UMI-tagged data. MAGERI implements consensus assembly, alignment and variant calling and allows to process datasets into ready SAM and VCF files in a single command. Its main purpose is to analyze targeted region genome re-sequencing data for tumor heterogeneity and circulating tumor DNA studies, however it can be also applied to other tasks that require accurate rare variant detection. See mageri-paper repository for examples and supplementary data.

bioinformatics cancer umi variant mutation mapping amplicon exon ctdna

migec - A RepSeq processing swiss-knife

•    Groovy

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This pipeline provides several useful tools for analysis of immune repertoire sequencing data. Its main feature is the ability to use information from unique nucleotide tags (UMIs, see this paper for details), which are attached to molecules before sequencing library preparation and allow to backtrack the original sequence of molecule. UMIs make it possible to computationally filter nearly all experimental errors from resulting immune receptor sequences. This pipeline was designed for libraries sequenced using Illumina MiSeq and HiSeq and the main requirement for sequencing reads is that they should contain the entire CDR3 region of immune receptor gene. Sequencing libraries with high over-sequencing, i.e. ones that have 5+ reads per starting molecule (unique UMI tag), should be used for optimal error elimination.

bioinformatics ngs sequencing adapter umi immunology antibody rep-seq

egg-view-assets - Manage frontend assets in development and production.

•    Javascript

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Manage frontend assets in development and production. Configuration, you can see full example in egg-ant-design-pro.

eggjs egg assets egg-view webpack roadhog umi eggplugin egg-plugin

fgbio - Tools for working with genomic and high throughput sequencing data.

•    Scala

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A set of tools to analyze genomic data with a focus on Next Generation Sequencing. This readme document is mostly for developers/contributors and those attempting to build the project from source. Detailed user documentation is available on the project website including tool usage and documentation of metrics produced. Detailed developer documentation can be found here. For a full list of available tools please see the tools section of the project website.

analyzing-genomic-data umi bioinformatics ngs

zUMIs - zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

•    R

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zUMIs is a fast and flexible pipeline to process RNA-seq data with (or without) UMIs. The input to this pipeline is simply fastq files. In the most common cases, you will have a read containing the cDNA sequence and other read(s) containing UMI and Cell Barcode information. Furthermore, you will need a STAR index for your genome and GTF annotation file.

rnaseq rna-seq single-cell umi expression barcodes fastq dge pipeline

umi-plugin-md - 🍚 Markdown(*.md) component plugin for umi.

•    TypeScript

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Markdown(*.md) component plugin for umi. Create your website with umi and markdown only. Convenient and powerful for blog, documentation site and GitBook.

umi markdown component umi-plugin

umi-dva-antd-starter - Get started with Umi.js and Ant Design.

•    Javascript

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Get started with Umi.js and Ant Design. Install dependencies.

dva starter ant-design react umi

rumi - Rust UMI Directional Adjacency Deduplicator

•    Rust

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Rust UMI based PCR deduplication based on the directional adjacency as UMI-tools but with a constant time hamming distance implementation. For now this relies on the rust toolchain. There are excellent docs on how to set that up.

bioinformatics algorithms umi