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Variantconvert ⭐ 9

A customizable genetic variants file format converter.

Fastqwiper ⭐ 9

An ensamble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and fix reads interleaving.

Ngs_workshop_advanced_bioinformatics ⭐ 9

Tophat Recondition ⭐ 9

Post-processor for TopHat unmapped.bam files making them useable by downstream software.

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Docker Ngs Tools ⭐ 8

A catalogue of docker images for NGS data analysis tools

Nanosim H ⭐ 8

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

SEAL db - Simple, Efficient And Lite database for NGS

Rs_demultiplex ⭐ 7

Simple demultiplexing of FASTQ, one oligo (barcode) at a time

Staph B.github.io ⭐ 7

Visit the site here: https://staphb.org

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

Microhapdb ⭐ 7

Portable database of microhaplotype marker and allele frequency data

Procedure used fro the surveillance of SARS-CoV-2 genomic variants in wastewater.

HTSinfer infers metadata from Illumina high throughput sequencing (HTS) data

genotyping by Mapping-free ALternate-allele detection of known VAriants

Tumor-only variant calling

Nanoforms ⭐ 6

The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer

Microhapulator ⭐ 5

Tools for empirical microhaplotype calling, forensic interpretation, and simulation.

Kcri Cge Bap ⭐ 5

KCRI CGE Bacterial Analysis Pipeline

Decontaminer ⭐ 5

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS da

Automated Pipeline for Variant/Haplotype Calling and Filtering

Fastq To Bam ⭐ 5

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

A fully integrated K-mer Informed Toolkit for Bioinformatics

Stringmeup ⭐ 5

A post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.

Vizsnp St ⭐ 5

Visualizing the effect of SNPs on protein structure using iCn3D

Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow

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