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23 search results found

Fastp ⭐ 1,602

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

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Strobealign ⭐ 114

Aligns short reads using dynamic seed size with strobemers

Taxprofiler ⭐ 78

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Command line utility for manipulating Illumina-generated FASTQ files.

Sample Sheet ⭐ 45

Parse Illumina sample sheets with Python

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

ClairS - a deep-learning method for long-read somatic small variant calling

Awesome Sequencing Tech Papers ⭐ 26

A collection of publications on comparison of high-throughput sequencing technologies.

Ngs Preprocess ⭐ 23

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Seqmaker.jl ⭐ 19

(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

Clairs To ⭐ 18

ClairS-TO - a deep-learning method for tumor-only somatic SNV calling

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

S4 Clarity Lib ⭐ 16

A modern Python library for BaseSpace Clarity LIMS.

Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS

Grandeur ⭐ 13

UPHL's Reference Free Pipeline

Digestiflow Server ⭐ 13

🍸 Web-based database system for flow cell management (incl. REST API)

Chimerate ⭐ 12

A pipeline to detect chimeric transcripts derived from genes and transposable elements.

16s Rdna V3 V4 ⭐ 8

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

Automated Tool for Global Screening Array analysis

Ampligone ⭐ 6

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

A web app for environmental DNA metabarcoding analysis

A fully integrated K-mer Informed Toolkit for Bioinformatics

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