Jit
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P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2949 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
By Jit 2485 days agoacademic.oup.com - The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 940 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
By Abhi 3812 days agohttp://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...Samtools Primer !!
By Jit 3755 days agobiobits.org - SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions 1.0: May 30, 2013: First public release on...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3490 days agoStructural variation caller tools using long readsASAR: Advanced metagenomic Sequence Analysis in R
By Jit 3009 days agogithub.com - An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3224 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2287 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 2393 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...
