Allows investigation of Iso-Seq data. TAPIS aims to correct errors, align reads to the reference genome, find all splice isoforms and alternative splicing (AS) events generated from a gene and 3’ heterogeneities because of alternative polyadenylation (APA) sites. It represents an iterative process that alternates read mapping and error correction on the basis of the reference genome. This tool is able to cooperate a two-stage error-correction in the neighbourhood of splice junctions.
Provides a solution for isoform sequencing (Iso-Seq) analysis. PRAPI can process: (1) alternative transcription initiation (ATI), (2) alternative cleavage and polyadenylation (APA), (3) alternative splicing (AS), (4) circular RNA and (5) natural antisense transcripts (NAT). This software supports also new genes annotations mis-annoted genes correction. The results are displayed to users via vector graphics.
Allows correction of microindels, mismatches, and noncanonical splice junctions in mapped transcripts using the reference genome while preserving known variants. TranscriptClean is a program using the reference genome, splice annotation, and a variant file to perform these corrections. This tool aids researchers to process transcripts in the SAM format, scanning each entry to look for insertions, deletions, and mismatches relative to the reference genome.
Consists in a transcriptome sequencing and analysis strategy. ToFU enables generation of de novo transcriptome from PacBio reads, deleting the need for short-read assembly or reference genomes. It aims to bypass complicated experimental and informatic procedures of short-read assembly and instead leverage the longest reads from the PacBio platform to yield high-confidence transcript isoforms independent of a reference genome.
Allows determination of the full-length transcripts of highly similar multicopy gene families. IsoCon enables error-correction and removes redundancy of PacBio circular consensus sequence (CCS) reads generated from targeted sequencing with the Iso-Seq protocol. The software consists of two main steps: (i) an iterative clustering algorithm to error-correct the reads and identify candidate transcripts, and (ii) iterative removal of statistically insignificant candidates. It can capture transcripts that differ by only one nucleotide in sequence and by three orders of magnitude in abundance.
Provides a platform dedicated to Iso-Seq data management. ISB is a standalone software that permits users to view and cluster long-read RNA sequencing data. The application includes multiple features for comparing and filtering novel gene isoforms and reference transcripts. In addition, it also provides customization functionalities that allows researchers to generate graphical supports for publication and facilities for export the output data.
Assists users to manage variable error rates. isONclust is an algorithm for clustering long reads according to their gene family of origin. This program was tested on on three simulated and five biological datasets, across a breadth of organisms, technologies, and read depths. It processes on two steps: (1) it finds the number of minimizers shared with each of the current representatives; and (2) it uses a minimizer-based method to try to assign a read to one of the candidate representative’s cluster.