Installed This software should be available with no extra configuration. SANS-2.2_04A Symmetric Alignment-free phylogeNomic Splits — Space and time Efficient Re-Implementation including Filters Reference-free Alignment-free Assembled genomes or reads as input Phylogenetic splits or tree as output NEW: Coding sequences / amino acid sequences as input (see –code and –amino), implemented by Marco Sohn Details on filter option The sorted list of splits is greedily filtered, i.

Installed This software should be available with no extra configuration. fastp 0.23.2 A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. features comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents…) filter out bad reads (too low quality, too short, or too many N…) cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).

Conda See the ‘activating the conda environment’ section below to access this software. salmon-1.9.0 Try out the new alevin-fry framework for single-cell analysis; tutorials can be found here! Help guide the development of Salmon, take our survey What is Salmon? Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference.

Conda See the ‘activating the conda environment’ section below to access this software. SQANTI3-5.1.0 SQANTI3 is the newest version of the SQANTI tool that merges features from SQANTI and SQANTI2, together with new additions. SQANTI3 will continue as an integrated development aiming to provide the best characterization for your new long read-defined transcriptome. SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, which also includes IsoAnnot and tappAS.

STAR - Spliced Transcripts Alignment to a Reference Abstract Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.

SQANTI3 SQANTI3 is the newest version of the SQANTI tool that merges features from SQANTI and SQANTI2, together with new additions. SQANTI3 will continue as an integrated development aiming to provide the best characterization for your new long read-defined transcriptome. SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, which also includes IsoAnnot and tappAS. Latest updates Latest SQANTI3 release (01/06/2022) is version 5.0. WARNING: v5.0 constitutes a major release of the SQANTI3 software.