Genome Biology Computational Support

[GALAXY] New tools

Author: Jelle - Published At: 07-05-2015 16:44 - (1487 Reads)

In the last weeks/months, we have installed and updated a bunch of Galaxy tools:

- Liftover to change your genomic coordinates e.g. from mm9 to mm10

- The Picard tool suite has been updated and expanded. For example, the following tools are now available: Downsample SAM/BAM, CleanSam, AddCommentsToBam, ValidateSamFile, EstimateLibrarySizeComplexity

- The full Bedtools suite is now available. Tools incl. SlopBed, ClosestBed and WindowBed

- Filter BAM, which allows you to filter multi-mapping reads obtained in PE experiments. Tool written by Charles Girardot.

- Update/new regional variation tools:

- Fetch Indels from 3-way alignments

- Indel Realigner - perform local realignment

- Estimate Indel Rates for 3-way alignments

- Delete Overlapping Indels from a chromosome indels file

- Fetch Indels from pairwise alignments

- Cuffcompare, Cufflinks, Cuffdiff and Cuffmerge run version 2.2.1 now

- NFS Transfer has been updated

- Compute_motif_frequencies_for_all_motifs and compute_motifs_frequency are back

- The converters: bigwig_to_wig and bam_to_bigwig have been added

- The deeptools package updated to version 1.5.9.1

- Added CEAS to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq