81 Open source projects that are alternatives of or similar to ngsLD

Utilities for analyzing next generation sequencing data.

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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

RNA-seq workflow using STAR and DESeq2

An automated RNA-seq pipeline using Nextflow

A method for variant graph genotyping based on exact alignment of k-mers

Multi-sample somatic variant caller

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

A robust model for quantitative comparison of ChIP-Seq data sets.

Tools to process and analyze deep sequencing data.

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

NGLess: NGS with less work

A library for manipulating bioinformatics sequencing formats in Apache Spark

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

Official code repository for GATK versions 4 and up

🐳 Bio-dockers: dockerized bioinformatic tools

Transposon Insertion Finder - Detection of new insertions in NGS data

A workflow for creating small NGS test data sets, useful for continuous integration.

Data intensive science for everyone.

Ultrafast sequence typing and gene detection from NGS raw reads

Customizable workflows based on snakemake and python for the analysis of NGS data

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

A collection of Galaxy-related training material

Localization Distillation for Dense Object Detection (CVPR 2022)

Tools for working with genomic and high throughput sequencing data.

myVCF: a web-based platform for target and exome mutations data management

R package for analyzing single-cell RNA-seq data

Population-wide Deletion Calling

UGENE is free open-source cross-platform bioinformatics software

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Sequana: a set of Snakemake NGS pipelines

Collection of scripts for bacterial genomics

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Exome/Capture/RNASeq Pipeline Implementation using snakemake

ABRA2

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Faster BWA-MEM2 using learned-index

Estimation of per-individual inbreeding coefficients under a probabilistic framework

An easy-to-use way for running Galaxy workflows.

(No maintenance) Detect gene fusion directly from raw fastq files

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

Estimation of pairwise distances under a probabilistic framework

Rare variant test software for next generation sequencing data

C library for high-throughput sequencing data formats

A library to integrate launch darkly with react redux

Java utilities for Bioinformatics

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

A simplified pipeline for ctDNA sequencing data analysis

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Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.

A Java API for high-throughput sequencing data (HTS) formats.

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

An Efficient Swiss Army Knife for Population Genomic Analyses in R

My bioinfo toolbox

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.