ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree an...n H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome...1720 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome...1715 days ago
Gooey: Turn (almost) any Python command line program into a full GUI application with one line
Turn (almost) any Python command line program into a full GUI application with one li...pip pip install Gooey Alternatively, you can install Gooey by cloning the project to your local directory git...1710 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a...or above a given threshold for each chromosome and genome-...1695 days ago
1684 days ago
simuG: a general-purpose genome simulator
Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioi...man). The simplicity and versatility of simuG make it a unique general-purpose genome...1683 days ago
RepeatModeler2: automated genomic discovery of transposable element families
RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome...1679 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
The Docker image is available at https://hub.docker....s well as test data are publicly accessible at the project documentation site http:...ilable via the GigaScience database GigaDB • Project name: SeQuiLa-cov • Pro...1666 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not...pondence for each heterozygous variant called on a phased reference genome....1662 days ago
1658 days ago