We are pleased to announce the beta release of new tool called SRMA: the short read micro re-aligner. We have tested this method on human cancer resequencing datasets as well as performed validation with simulations. We wish to find beta testers to provide feedback and suggest new features to the tool.
Link:
Short description:
Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus.
Features:
- The input is a BAM, the output is BAM.
- Specify a co-ordinate range for large-scale parallelism or local regions of interest.
- SOLiD data is re-aligned using the original color space reads and qualities to maximally use all information available (SAM CS/CQ tags must be present).
- A base correction mode for Illumina/454 data automatically recalls bases in the reads based on all alignments, removing spurious variants and adjusting their respective base qualities.
Acknowledgments:
Thanks to the Picard team for their fast responses to questions about the SAM/BAM Picard API. We would also like to thank the members of the Nelson Lab at UCLA.
Sincerely,
Nils Homer
Link:
Short description:
Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus.
Features:
- The input is a BAM, the output is BAM.
- Specify a co-ordinate range for large-scale parallelism or local regions of interest.
- SOLiD data is re-aligned using the original color space reads and qualities to maximally use all information available (SAM CS/CQ tags must be present).
- A base correction mode for Illumina/454 data automatically recalls bases in the reads based on all alignments, removing spurious variants and adjusting their respective base qualities.
Acknowledgments:
Thanks to the Picard team for their fast responses to questions about the SAM/BAM Picard API. We would also like to thank the members of the Nelson Lab at UCLA.
Sincerely,
Nils Homer
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