170 Open source projects that are alternatives of or similar to alignment-nf

Multi-sample somatic variant caller

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Collection of scripts for bacterial genomics

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

🐳 Bio-dockers: dockerized bioinformatic tools

Estimation of pairwise distances under a probabilistic framework

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

C library for high-throughput sequencing data formats

Ultrafast sequence typing and gene detection from NGS raw reads

Java utilities for Bioinformatics

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

A simplified pipeline for ctDNA sequencing data analysis

Faster BWA-MEM2 using learned-index

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

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

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Helpful components for aligning and keeping virtual objects aligned with the physical world.

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

uLTRA is a long-read splice aligner with high accuracy from using a guiding annotation

Method to optimally select samples for validation and resequencing

Detect novel (and reference) STR expansions from short-read data

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

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

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Displayed width of UTF-8 strings in Modern C++

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

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Reference-based transcript discovery from long RNA read

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Sentieon DNAseq

My bioinfo toolbox

[CVPR'19] Dataset and code used in the research project Scan2CAD: Learning CAD Model Alignment in RGB-D Scans

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

TCSVT2018 Pedestrian Alignment Network for Large-scale Person Re-identification

Nightlight: Astronomic Image Processing

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

A collection of Galaxy-related training material

SDK for GPU accelerated genome assembly and analysis

Docker for 4DN Hi-C processing pipeline

MTCNN Face Detection & Alignment

Tools for working with genomic and high throughput sequencing data.

aeneas is a Python/C library and a set of tools to automagically synchronize audio and text (aka forced alignment)

Flexible Algorithms for Image Registration

The official PyTorch implementation of Towards Fast, Accurate and Stable 3D Dense Face Alignment, ECCV 2020.

R package for analyzing single-cell RNA-seq data

Code repo for "Spatio-Temporal Filter Adaptive Network for Video Deblurring" (ICCV'19)

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

A curated list of awesome resources for image alignment and stitching ...

UGENE is free open-source cross-platform bioinformatics software

RStudio addin for formatting Rmarkdown tables

A library for manipulating bioinformatics sequencing formats in Apache Spark

Sequana: a set of Snakemake NGS pipelines

A scalable bacterial genome assembly, annotation and analysis pipeline

Nanopore demultiplexing, QC and alignment pipeline

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

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

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

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