maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.

主要是关于各类高性能计算软件安装的文档

openEuler High Performance Computing(HPC)

Weather Research and Forecasting Model

SU2 is a suite of open-source software tools written in C++ for the numerical solution of partial differential equations (PDE) and performing PDE constrained optimization. The primary applications are computational fluid dynamics and aerodynamic shape o...

The 3D-DNA pipeline was used to error-correct, anchor, order and orient the pieces in the draft assembly. The 3D-DNA visualization module, in conjunction with Juicer Tools, was used to create contact maps for the draft and the final genome assemblies.

The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program.Subread aligner can be used to align both gDNA-seq and RNA-...

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, ...

Redundans pipeline assists an assembly of heterozygous genomes. Program takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly.

A probabilistic framework for structural variant discovery.

rMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of rMATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions ...

RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary compu...

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

genewise: a program for aligning proteins or protein HMMs to DNA, and dynamite a rather cranky "macro language" which automates the production of dynamic programming.