SPAdes Genome Assembler
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Updated
Sep 26, 2024 - C++
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
Transcriptome assembly via digital normalization with khmer and Trinity
Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining
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
Assembler for multiple RNA-seq samples
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
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