pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
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Updated
Dec 27, 2022 - Python
pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data
a core part of the MiModD package for use as a library
Implementation of the Analytic Hierarchy Process (AHP) to obtain the immunogenicity score of wheat lines based on their celiac disease (CD) epitopes matches on alpha- and gamma-gliadins amplicons by NGS and the score for oligopeptides based on an IFN-g ELISpot assays with fresh peripherical blood mononuclear cells (PBMCs).
A collection of various tools useful for the deep analysis of data generated via the CRSSANT/rna2d3d pipeline.
Different approaches to calculate mappability and GC-rich tracks for danio rerio genomes
project for developing python package to handle ngs data
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).
Filters for Next Generation Sequencing
Determine polyA sites from 3'end sequence data
Various tools for the analysis and manipulation of FASTA and FASTQ files.
Associate outliers with rare variation
Companion code for "Very fast CRISPR on demand"
Structural variant calling and functional annotation in five mice lines selected for specific traits and a control line.
A LatchBio workflow for running Kraken2
A front-end GUI to map NGS DNA sequencing data using HISAT backend tool. This software offers robust seamless queueing of the mapping operations along with parameter memory for quick and easy customization.
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