Results for "Assembly"
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RNA-Seq De novo Assembly Using Trinity
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied seq...Tags: Bioinformatics, NGS, RNA-seq, Assembly, Trinity, Illumina
2966 days ago
- Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI). More at http://eas...
Tags: Bioinformatics, NGS, Assembly, View, Fig, Easyfig, Tool
2929 days ago
PAired-eND Assembler for DNA sequences
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseqTags: Bioinformatics, NGS, Assembly, Paired-End, PANDASEQ, Illumina
2952 days ago
- MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by electrophoresis sequencing (aka Sanger sequencing) 454 pyro-sequencing (GS20, FLX or Titanium) Ion Torrent Solexa (Illumina) sequencing ...
Tags: Bioinformatics, NGS, Assembly, Paired-End, MIRA, Illumina
2952 days ago
RACA: Reference-Assisted Chromosome Assembly
Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. http://www.ncbi.nlm.nih.gov/pubmed/23307812 http://bioen-comp...Tags: Bioinformatics, NGS, Assembly, Reference, RACA, Reads
2952 days ago
QUAST: quality assessment tool for genome assemblies
QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies, thus is suitable for comparison. More at http://bioinf.spbau.ru/quast http://bioinformatics.oxfordjou...Tags: Bioinformatics, Computational Biology, Assembly, Comparison, Accuracy
2951 days ago
REAPR: a universal tool for genome assembly evaluation
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual insp...Tags: Bioinformatics, Computational Biology, Assembly, Comparison, Accuracy, Evaluation
2951 days ago
- Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at http://www.bioinformatics.babraham.ac.uk/projec...
Tags: Bioinformatics, NGS, Assembly, Quality, FastQC, Tutorial
2943 days ago
- DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or longer — produced on MiSeq or HiSeq 2500 &m...
Tags: Bioinformatics, NGS, Assembly, DISCOVAR, Variants, BroadInstitute
2939 days ago
