DendroPy: a Python library for phylogenetic computing
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogen...2218 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2187 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data Afte...bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/300...2151 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of:...ll, manageable subsets which can then be assembled quickly and efficiently in parallel....2124 days ago
NanoPack: visualizing and processing long-read sequencing data
The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together...2108 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel....2033 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of variant...er purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be writt...2033 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
SAMStat is an efficient C program to quickly display statistics of large sequence file...ausing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipel...2018 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
Given the potential relevance of efficient haplotyping in several analysis pipelines,...we have designed and engineered pWhatsHap, a parallel, high-performance version of&...s exponential in the coverage of the dataset. The parallel i...2013 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences,...omputation of sequence families with low time and space requirements. A parallel v...1985 days ago