SPAdes Genome Assembler

de novo assembly of RNA-seq data using ABySS

A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

Quality assessment of de novo transcriptome assemblies from RNA-Seq data

Official Repository of the Oyster River Protocol for Transcriptome Assembly

Finding putative exons and constructing splicegraphs using Trans-ABySS contigs

Emending Alignment of Spliced Transcript Reads

Most up-to-date scripts used in the Palumbi lab

QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.

Assembler for multiple RNA-seq samples

A collection of scripts for our PacBio paper

Scripts and notes related to the manuscript: Stuart KC & Edwards RJ et al. 2022. Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology Resources, doi.org/10.1101/2021.04.07.438753. † joint first author

tool for long read transcriptome assembly

Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

Transcriptome assembly via digital normalization with khmer and Trinity

Biocore's de novo transcriptome assembly workflow based on Nextflow

A pipeline for the assembly of VAR genes from transcriptome data

A collection of scripts for our PacBio paper

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

MuSTA: Multi-Sample Transcriptome Assembly for long-read isoform sequencing