Results for "Pipeline"
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PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pa...Tags: PGAP-X, Extension, pan-genome, analysis, pipeline
2319 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together. Reducing/removing reference bias as compared to mapping...Tags: ARC, pipeline, facilitates, iterative, reference, guided, de novo, assemblies
2136 days ago
- An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites o...
Tags: MetaPlotR, Perl, R, pipeline, plotting, metagenes, nucleotide, modifications, transcriptomic, sites
2034 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional arguments:positive_seq the fasta file for the po...Tags: pipeline, find, motifs, fasta
1965 days ago
- Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless distribution of tasks over local or distribute...
Tags: Katuali, flexible, consensus, pipeline, Snakemake, basecall, assemble, polish, Oxford, Nanopore, Technology, sequencing, data
1956 days ago
- Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975
Tags: CAUSEL, epigenome, genome, editing, pipeline, function, noncoding, GWAS, variants
1879 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative fu...Tags: multiPhATE, bioinformatics, pipeline, functional, annotation, phage, isolates
1842 days ago
dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not requ...Tags: dnaPipeTE, pipeline, find, annotate, quantify, Transposable, Elements, TEs
1753 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range o...Tags: TRITEX, sequence, assembly, pipeline, Triticeae, genomes
1746 days ago
