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勇者无敌 - 智者无惧 - 仁者无忧
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.
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 optimization, but has been extended to treat more general equations such as electrodynamics and chemically reacting flows.
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 exceeds a given user-defined threshold. From the RNA-Seq data, rMATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. rMATS handles replicate RNA-Seq data from both paired and unpaired study design.
Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome assembly. Currently, Flye will produce collapsed assemblies of diploid genomes, represented by a single mosaic haplotype. To recover two phased haplotypes consider applying HapDup after the assembly.
