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

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

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

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

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

Assembler for multiple RNA-seq samples

tool for long read transcriptome assembly

Biocore's de novo transcriptome assembly workflow based on Nextflow

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

A collection of scripts for our PacBio paper

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

Visualize read-to-contig alignment during assembly analysis

A pipeline for the assembly of VAR genes from transcriptome data