Apollo: a sequence annotation editor
The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological exp...ollo was developed to meet this need, enabling curators to inspect genome...1777 days ago
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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...1716 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
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...1684 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...1680 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....1663 days ago
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