43 Open source projects that are alternatives of or similar to pm4ngs

Utilities for analyzing next generation sequencing data.

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Finds SNP sites from a multi-FASTA alignment file

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

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

Rare variant test software for next generation sequencing data

Software for exploration of gene expression data from single-cell RNA sequencing.

A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

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.

Assembling the cause of phenotypes and genotypes from NGS data

My own tools code for NGS data analysis (Next Generation Sequencing)

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Command line utility for manipulating Illumina-generated FastQ files.

Multilocus sequence typing by blast using the schemes from PubMLST

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Improve the quality of a denovo assembly by scaffolding and gap filling

Minor Variant Calling and Phasing Tools

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Regulatory networks with Direct Information in python

Compare different differential abundance and expression methods

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

A proof of concept of RNAseq pipeline

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Import and summarize transcript-level estimates for gene-level analysis

A proof of concept RNA-Seq pipeline with Nextflow

Modeling and correcting fragment sequence bias for RNA-seq

Analysing Capture Seq Count Data

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Ultrafast sequence typing and gene detection from NGS raw reads

Metagenomic pipeline and other general scripts used in the lab.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources