113 Open source projects that are alternatives of or similar to IMPACT-Pipeline

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

NGLess: NGS with less work

Official code repository for GATK versions 4 and up

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

Collection of scripts for bacterial genomics

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

My bioinfo toolbox

Rare variant test software for next generation sequencing data

Transposon Insertion Finder - Detection of new insertions in NGS data

Data intensive science for everyone.

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

An automated RNA-seq pipeline using Nextflow

RNA-seq workflow using STAR and DESeq2

A novel management, annotation, and machine learning framework for analyzing cancer mutations

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

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

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

Multi-sample somatic variant caller

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

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

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

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

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

Tools to process and analyze deep sequencing data.

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

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

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

A collection of Galaxy-related training material

No description or website provided.

Tools for working with genomic and high throughput sequencing data.

A simplified pipeline for ctDNA sequencing data analysis

R package for analyzing single-cell RNA-seq data

Exome/Capture/RNASeq Pipeline Implementation using snakemake

UGENE is free open-source cross-platform bioinformatics software

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

Sequana: a set of Snakemake NGS pipelines

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

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

Single-cell copy number calling and event history reconstruction.

ABRA2

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

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

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.

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Backend Server for CIViC Project

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

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

Estimation of pairwise distances under a probabilistic framework

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

C library for high-throughput sequencing data formats

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

Java utilities for Bioinformatics

Initial data release for drug-target interactions of the cancer targetome.

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

🐳 Bio-dockers: dockerized bioinformatic tools

A library for manipulating bioinformatics sequencing formats in Apache Spark

Ultrafast sequence typing and gene detection from NGS raw reads

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

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