Inchworm is now incorporated into the full Trinity RNA-Seq assembly package. Inchworm will still be maintained here for the time being since Trinity hasn’t been fully incorporated into genome-guided assembly and PASA-based genome annotation yet.

The inchworm RNA-Seq assembler, developed at the Broad Institute, employs the Kmer graph method to reconstruct (in many cases full-length) transcripts from Illumina RNA-Seq (preferrably strand-specific) reads. Inchworm is especially effective when used with strand-specific RNA-Seq data.

Download the current software here.

Inchworm Installation

Install by running:

configure --prefix=`pwd`
make install

Running Inchworm

RNA-Seq assembly using Inchworm an proceed either of two ways:

  • De novo assembly : Transcripts are reconstructed based on the read sequences alone. Documentation is provided here: Inchworm De novo Assembly.

  • Genome-guided assembly : RNA-Seq reads are first aligned to the genome. Reads are clustered according to covered regions of the genome, and Inchworm de novo assembly is performed on each partition separately. This method is advantageous if you have a high quality genome assembly to work from. We provide a BLAT-based read alignment pipeline that we find to be particularly effective with RNA-Seq reads at least 67 bases in length, but alternative alignment methods can be employed as well, such as TopHat. Documentation is provided here: Genome-guided Inchworm Assembly.

Annotating Eukaryotic Genomes using RNA-Seq

The PASA Pipeline software can leverage Inchworm transcriptome assemblies for eukaryotic gene structure annotation. Documentation is provided at .

Strand-specific Illumina RNA-Seq (Preferred)

It is now relatively straightforward to generate strand-specific RNA-Seq data via Illumina. Given the great utility of strand-specific data in differentiating between sense and antisense transcription, plus given the great depth of transcriptome sequencing coverage and the great prevalence of antisense transcription, strand-specific RNA-Seq should be pursued whenever possible. The dUTP strand-specific RNA-Seq method by Parkhomchuk et al., NAR, 2009 is recommended. For a comparison of strand-specific methods, see Comprehensive comparative analysis of strand-specific RNA sequencing methods. by Levin et al, Nat Methods, 2010.

Software Support

For support, email to at: .