Python script for comparing two genome assemblies
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Updated
Jan 22, 2018 - Python
Python script for comparing two genome assemblies
preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.
[FCCM 2019] Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: A Race Between FPGA and GPU
Third generation sequencing techniques rapidly evolved as a common practice in molecular biology. Great advances have been made in terms of feasibility, cost, throughput, and read-length. However, sample contamination still poses a big issue: it complicates correct, high-quality downstream analysis of sequencing data and usage in medical applica…
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
Genopo a.k.a. F5N - a portable DNA analysis toolkit for nanopore data https://nanoporetech.com
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
Simple Alignment Viewer
Scalable and High Performance Variant Calling on Cluster Environments
A lightweight library for working with PAF (Pairwise mApping Format) files
The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https…
Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.
SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.o…
Real-time species-typing visualisation for nanopore data.
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.
This repository streamlines the conversion of raw DNA sequencing data from FASTQ to BAM format, incorporating scripts that not only facilitate BAM conversion but also generate Sequence Alignment Map (SAM) files.
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