WhatsHap: fast and accurate read-based phasing
..., but works also well with short reads. Features Very accurate results (Martin et al., WhatsHap...ng mode uses reads from related individuals (such as trios) to improve results and to reduce coverage requir...2179 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
...y go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Cur...2147 days ago
ASAR: Advanced metagenomic Sequence Analysis in R
...etagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available. To read the ma...2137 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those rea...2120 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
...analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results. https://f1000research.com/a...2108 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and...2035 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...learning algorithms that address these shortcomings have the potential to achieve better and more accurate integration of these two technologies. Results: We designed and developed He...2095 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and inse...2095 days ago
2056 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a re...2035 days ago