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[[Category:Software]][[Category:Biology]][[Category:Transcriptome]] ...ector, is a software that has two sub-pipelines to jointly analyze of host transcriptome with its microbiome by using bulk RNA-seq and single-cell RNA-seq data, res ...

...ion that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance a ...

...unts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clust ...

Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares .../2015/06/27/021626 TransRate: reference free quality assessment of de-novo transcriptome assemblies. Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibb ...

HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. ...

...lts demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants. ...

...or identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. TALON is technology-agnostic in that it works from mapped SAM fi A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification. Dana Wyman, Gabriela Balderrama-Gutierrez, Fa ...

...y consumption is around 5Gb for 100M reads. KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the trans ...

...e script BYO_transcriptome.py, which can be used to add sequences from any transcriptome to any protein-coding nucleotide target file. These tailored and customised ...

eliminating the need for transcriptome reconstruction using within targeted genes or the entire transcriptome. ...

TACO: Multi-sample transcriptome assembly from RNA-Seq ...

Description: Eukaryote Non-Model Transcriptome Annotation Pipeline ...

Description: a transcriptome assembly and mRNA annotation pipeline ...

rnaQUAST is a tool for evaluating quality of transcriptome assemblies using reference genome and gene database. ...

FUSION is a suite of tools for performing a transcriptome-wide (or any other ome-wide) association study by predicting functional/mol ...

SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing ...

...e information rich basecalling neural network output to a reference genome/transcriptome. ...

dammit is a simple de novo transcriptome annotator. It was born out of the observation that: annotation is mundane a ...

...ions are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfa ...

...a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where the ...

...ation of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res. 2018;28(3):396-411. doi:10.1 ...

...r reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. ...

...large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneo ...

...Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genom ...

...i Z. (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453] ...

Oases is a de novo transcriptome assembler designed to produce transcripts ...

STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify cand ...

...9 Kristoffer Sahlin, Paul Medvedev (2019) "De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm", Journal of Computation ...

...fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh-frozen tissues to disc ...

...: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res (2017). doi:10.1093/nar/gkw1306] ...

...es possible highly accurate RNA secondary structure modeling on genome and transcriptome wide scales. ...

IDBA-MT is an iterative De Bruijn Graph De Novo short read assembler for meta-transcriptome. It is purely de novo assembler based on paired-end RNA sequencing reads on ...

Bridger is an efficient ''de novo'' transcriptome assembler for RNA-Seq data. It expects as input RNA-Seq reads (single or pa ...

...scientific hypothesis or a means to create a whole annotation report for a transcriptome. ...

...igned for compact storage and efficient analysis of multi-genome and multi-transcriptome datasets. The programs provided in MVFtools support this format, both with ...

deSALT(de Bruijn graph-based Spliced Aligner for Long Transcriptome reads) ...

...reference sequence(s) can be whole genomes with multiple chromosomes, the transcriptome or even the millions reads in the fasta format, separated by '>'. The reads ...

...offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolution ...

...t VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequenci ...

...equences from your own Fungal biological data, including genome sequences, transcriptome sequences, and proteome sequences. ...

...quantification of gene or isoform abundance is a fundamental step in many transcriptome analysis tasks, such as determining differential expression between biologi ...

PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. Unlike conventional metho ...

...Caim S., Kaithakottil G., Mapleson D.L., Swarbreck D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. GigaScience, Volum ...

...ined for each. The method is accurate, simple and fast to execute and, for transcriptome data, requires low depth of coverage. Known HLA class I/class II reference ...

*-m or --mode sets the assessment MODE: genome, proteins, transcriptome ...