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Old 06-14-2011, 06:46 AM   #1
Fabien Campagne
Location: New York City

Join Date: Feb 2010
Posts: 39
Default Java framework+tools Goby 1.9.7 released (fast realign near indels & capture stats)

We have released Goby 1.9.7. This release has several new features, including the option to realign reads around indels on the fly when running one of the discover-sequence-variant analyses (allele frequency tests, group comparisons, etc.). We have designed a greedy realignment algorithm that is very efficient and require only moderate amounts of memory.

This release also includes a coverage tool. This tool can calculate coverage statistics for sequence capture designs efficiently. It uses the base-level histograms stored as counts files (basename.counts) produced by GobyWeb or the alignment-to-counts mode. This tool can estimate various depth of coverage statistics over capture regions in about 20 seconds for an alignment with about 30 million 100 bp aligned reads (e.g., human exome capture at ~20x coverage). Statistics include enrichment efficiency, coverage for specified percentiles, or percents of sites coverage at given depths. See this tutorial for details.

A new trim mode can remove adapters from either ends of reads. Works with single or paired-end data. When working with paired-end reads files, preserves order of sequences and existence of each sequence in a pair.

Goby 1.9.7 can also open an alignment when only the header file is present. This is useful to obtain alignment statistics or sequence identifiers without having to transfer the potentially much larger .entries files. A few bug fixes and performance improvements have also been implemented. For instance, this new version is orders of magnitude faster when parsing large VCF files.

See the change log for more details about this release.
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