Genome assembly forensics: finding the elusive mis-assembly
We present the first collection of tools aimed at automated genome assembly validatio...and highlight several assembly errors in both draft and finished genomes. The software described is compatible with...1985 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum like...s to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree1963 days ago
DISTRUCT: a program for the graphical display of population structure
distruct is a program that can be used to graphicall...and other graphical details. [Example] [Download software package (includes the manual)...ou register) [Download manual] [Download software note from Molecular Ecol...1928 days ago
OMTools: a software package for visualizing and processing optical mapping data
OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visu...1924 days ago
1909 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1806 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...tive metagenomics method dedicated to NGS datasets. https://gatb.inria.fr/software/simka/1825 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the...thms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware accele...1704 days ago
Seq: A high-performance, Pythonic language for bioinformatics
Seq is a programming language for computational genomics and bioinformatics....ecific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python cod...1685 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into po...genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuff...1486 days ago