Software

Hydra: structural variation discovery with paired-end-mapping.

Hydra detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose “signatures” corroborate the same putative breakpoint. More details…

BEDTools: fast tools for genome arithmetic

The BEDTools utilities allow one to address common “genome arithmetic” tasks such as finding feature overlaps, computing coverage, and merging, complementing and subtracting features. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by “streaming” several BEDTools together. The following are examples of common questions that one can address with BEDTools.

  1. Intersecting two BED files in search of overlapping features.
  2. Culling/refining/computing coverage for BAM alignments based on genome features.
  3. Merging overlapping features.
  4. Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
  5. Calculating the depth and breadth of sequence coverage across defined “windows” in a genome.
  6. Screening for overlaps between “split” alignments and genomic features.

The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets.

Stable releases: Major releases and use cases can be found here on Google Code.
Source code repository: The source code repository is housed here on GitHub.
Other realted software:
  • bedtools-python: A Cython-based Python interface to the core BEDTools API is also available here on GitHub
  • pybedtools: A convenient Python wrapper of the major BEDTools has been developed by Ryan Dale.

filo: useful file and stream operations

The filo suite is a collection of useful tools for manipulating text files and streams.  Documentation for the available tools can be found at the GitHub project site.

PyroBayes: accurate quality scores 454 pyrosequences

Coming soon.

Other:

Coming soon.

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