Genotyping from short reads using cloud computing

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Related Tools

    Bowtie: Ultrafast short read alignment
    Hadoop: Open Source MapReduce
    Contrail: Cloud-based de novo assembly
    CloudBurst: Sensitive MapReduce alignment
    Myrna: Cloud, differential gene expression
    Tophat: RNA-Seq splice junction mapper
    Cufflinks: Isoform assembly, quantitation
    SoapSNP: Accurate SNP/consensus calling

Reference jars

    H. sapiens: hg18/dbSNP 130
    M. musculus: mm9/dbSNP 128
    E. coli: O157:H7, NCBI (no SNPs)

Related publications


Other Documentation

  • WABI 09 Poster (.pdf)


Frequently Asked Questions

Does Crossbow support colorspace?

Yes, but note that the pre-built reference jars available from this site are currently all in nucleotide space. In the future, we will also post colorspace versions of the reference jars. That said, Crossbow works fine with colorspace reads: just ensure that you specify a colorspace reference jar and pass -C to Bowtie.

Can Crossbow handle a mix of colorspace and normal (nucleotide-space) reads in a single job?

No. As of now, Crossbow applies the same set of Bowtie arguments to every invocation Bowtie, and so cannot be used on both types of reads in the same job.

Can Crossbow output alignments in SAM or BAM format?

No. While Bowtie itself can certainly do this, Crossbow does not yet have a facility for outputting a directory of SAM/BAM files either as the final result or as an intermediate result.