BioStar
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BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2827 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
By Jit 2691 days agowww.zhanyuwang.xin - BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the...RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
By Jit 2324 days agogithub.com - 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 assembly contigs into...SPADes team announce new version SPADes v3.15
By BioStar 1878 days agoNew SPAdes 3.15.0.0. announced by the SPADes teamGenome Assembly Workshop 2020
By Jit 1656 days agoucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...ALE: Assembly Likelihood Estimator
By BioStar 1096 days agogithub.com - Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.Snakemake—a scalable bioinformatics workflow engine
By Jit 2743 days agobioconda.github.io - Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.
Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4616 days agoBarber pole worm , sheep pathogen sequenced !!!
By Rahul Agarwal 4568 days agoResearchers have uncovered essential information in the fight against drug resistance in worms.
