Data intensive science for everyone.
-
Updated
May 9, 2024 - Python
Data intensive science for everyone.
Infectious Disease Sequencing Platform
This repository summarizes complete NGS analysis for a beginner.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Graph-based assembly phasing
Mycobacterial pipeline
CLI tool for flexible and fast adaptive sampling on ONT sequencers
Simple & Efficient data access for Scala and Scala.js
Unified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)
SPAdes Genome Assembler
Official code repository for GATK versions 4 and up
Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Ancestry inference with convolutional neural networks
UGENE is free open-source cross-platform bioinformatics software
Visualization and analysis platform for metabolic data and network pattern recognition
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
a custom function which can be used to prepare the files for the genotyping or the sequencing. You can specify the path and the fasta files and mark them according to the desired condition for the genotyping or sequencing
making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.
Add a description, image, and links to the sequencing topic page so that developers can more easily learn about it.
To associate your repository with the sequencing topic, visit your repo's landing page and select "manage topics."