De novo transcriptome assembly software tools | RNA sequencing data analysis
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome.
Integrates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Galaxy permits users without programming skills to conduct computational analysis through the Web. It builds a succession of tools to perform multistep studies and is able to conserve the complete provenance of each analysis step. This platform offers drag and drop functionalities to ease the construction of workflows.
A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide Additional contigs can also be provided to be used as long reads. SPAdes supports paired-end reads, mate-pairs and unpaired reads and can take as input several paired-end and mate-pair libraries simultaneously.
Performs gene and isoform level quantification from RNA-Seq data. RSEM is a software package that quantifies gene and isoform abundances from single-end (SE) or paired-end (PE) RNA-Seq data. The software enables visualization of its output through probabilistically-weighted read alignments and read depth plots. It does not require a reference genome and can be used for quantifying de novo transcriptome assemblies.
Manipulates de Bruijn graphs (DBG) for genomic sequence assembly. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. It takes in short read sequences, removes errors, then produces high quality unique contigs uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. Velvet represents an approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
Builds transcriptomes from RNA-seq data. Trinity is a standalone software composed of three main components: (i) Inchworm, that first generates transcript contigs; (ii) Chrysalis, for clustering them and constructing complete de Bruijn graphs for each cluster and; (iii) Butterfly that processes individual graphs in parallel for finally resulting to the reconstruction of the transcript sequences.
The third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 58 and 38 low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences.