|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|
H. sapiens: hg18/dbSNP 130
M. musculus: mm9/dbSNP 128
E. coli: O157:H7, NCBI (no SNPs)
- Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10:R134.
- Schatz M, Langmead B, Salzberg SL. Cloud computing and the DNA data race. Nature Biotechnology 2010 Jul;28(7):691-3.
- Langmead B, Hansen K, Leek J. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 11:R83.
- Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
- Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SNP detection for massively parallel whole-genome resequencing. Genome Res. 2009. 19: 1124-1132.
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.