RopeBWT2: Incremental construction of FM-index for DNA sequences
RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by increment...ces. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonet...2047 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...les all statistics are reported for unmapped, poorly and accurately mapped reads separ...n of a variety of problems, such as remaining linker and...2032 days ago
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Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-sc...ad the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command! A short list of the new fea...l limits on the assembly completeness and...1989 days ago
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences can contain signifi...lies, designed to aid in identifying and correcting assembly errors. U...sembly along with summary statistics and assembly metrics, and are gui...project http://amos.sourceforge.net...1979 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from...hidden Markov model algorithm and a calling method that classif...te EXCAVATOR on three datasets and compare the results with thre...s well as in clinical research and diagnostics. EXCAVATOR is fre...ble at http://sourceforge.net...1976 days ago
Osprey: Network Visualization System
Osprey is a software platform for...ped by the TyersLab and is a part of the BioGRID...ware. It utilizes both MySQL and Java to operate and...tark, C., Tyers M. "Osprey: A Network Visualization System." Ge...nbsp;[PDF] [PubMed] and supported by the Nationa...1960 days ago
Genome assembly forensics: finding the elusive mis-assembly
We present the first collection of tools aimed at automated gen...ur pipeline in both bacterial and eukaryotic genome assemblies,...with common assembly formats and is released, open-source, at http://amos.sourceforge.net. https://www.ncbi.nlm.nih.go...bsp; http://amos.sourceforge.net...1954 days ago
dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testing1928 days ago
Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets
Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and... Genscale team at Inria. Contact: claire dot lemaitre at inria dot fr Simka and...1793 days ago