Morrell Lab software comparison table ====================================================== *************** | Software | lab version | MSI version | latest Version | URL | comments | is it up to date: Lab/MSI | | -------- | ----------- | ----------- | -------------- | --- | -------- | ---------- | | Bedtools | 2.26.0 (08-24-16) | 2.25.0 | 2.26.0 (07-06-16) | [Bed Tools](https://github.com/arq5x/bedtools2) | also installed: 2.23.0 | [X] [ ] | | Scythe | .994-BETA (08-25-16) | not in MSI | .994 | [Scythe](https://github.com/vsbuffalo/scythe) | .992 also installed | [X] [ ] | | BWA | 0.7.15 (08-08-14) | 0.7.12 | 0.7.15 (06-01-16) | [BWA](http://bio-bwa.sourceforge.net/) | pre versions: 7.10, 7.12 | [X] [ ] | | Bowtie2 | 2.29 (08-27-16) | 2.2.4 | 2.2.9 (04-22-16) | [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) |MSI also has Bowtie/2.2.4, Lab also installed: 2.21, 2.23, 2.26, 2.29 | [X] [ ] | | SAM Tools | 1.3.1 (08-25-16)) | 1.3 | 1.3.1 (04-22.16) | [SAM Tools](http://www.htslib.org/) | Pre-release version on githib: 1.5 | [X] [ ] | | Picard | 2.5.0 (08-26-16) | 2.3.0 (06-23-16) | 2.5.0 (06-23-16) | [Picard](http://broadinstitute.github.io/picard/) | Lab also installed: 1.118 | [X] [ ] | | ms | unknown updated: 08-25-16 | msff: 0.1.5 / msstats: 0.3.1 | unknown version - updated on 06-06-16 | [ms](http://home.uchicago.edu/rhudson1/source/mksamples.html) | none | [X] [ ] | | VCF Tools | 0.1.14 (08-25-16) | not in MSI | 0.1.14 | [VCF Tools](https://vcftools.github.io/downloads.html) | not in MSI | [X] [ ] | | GATK | 3.6 (08-27-16) | 3.3.0 | 3.6 (06-01-16) | [GATK](http://www.broadinstitute.org/gatk/) | Lab also installed: 3.2, 3.5 & 3.6 | [X] [ ] | | CAP3 | V-2015 | 3 | V-2015 | [CAP3](http://seq.cs.iastate.edu/) | Lab also installed:v-2013 | [X] [ ] | | Poly Phen 2 | 2.2.2r405a (07-18-16) | not in MSI | 2.2.2r | [Poly Phen2](http://seq.cs.iastate.edu/) | not in MSI | [X] [ ] | | Tablet | 1.15.09.01 (08-25-16) | not in MSI | 1.15.09.01 (09-01-15) | [Tablet](http://ics.hutton.ac.uk/tablet/) | not in MSI, Lab also installed: 1.14.04.10 | [X] [ ] | | Variant-Effect-Predictor | not stated (06-30-14) | not in MSI | web portal version: not stated, Pearl extension: release 84 (03-02-16) | [Variant-Effect-Predictor](http://ensembl.gramene.org/info/docs/tools/vep/index.html) | not in MSI | [ ] [ ] | | ANGSD & Htslib | angsd: .912, Htslib: 1.3.1 (08-27-16) | not in MSI | 0.912/0.913 (07/06/16) | [ANGSD](http://www.popgen.dk/angsd/index.php/Main_Page) | not in MSI, Lab also installed: angsd: .901 | [X] [ ] | | NGS Tools | 1.0.1 (08-28-16) | not in MSI | 1.0.1 (05-20-16) | [NGS Tools](https://github.com/mfumagalli/ngsTools) | not in MSI | [X] [ ] | | SRA Toolkit | 2.70 (08-27-16) | 2.5.4 | 2.7.0 (07-14-16) | [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software) | nLab also installed: 2.3.5-2 | [X] [ ] | | STRUCTURE | 2.3.4 (08-18-14) | 2.3.3 | 2.3.4 | [STRUCTURE](http://pritchardlab.stanford.edu/structure.html) | no updates since 2.3.4, MSI has latest but defaults to 2.3.3 | [X] [ ] | | FastX-Toolkit & Libtool | 0.0.14 , 2.2.6 (08-27-16) | 0.0.14 | 0.0.14 (01-5-14) | [FastX-Toolkit](http://hannonlab.cshl.edu/fastx_toolkit/download.html) | Lab also installed: FastX 0.0.6 | [X] [ ] | | Sickle | 1.33 | not in MSI | 1.33 | [Sickle](https://github.com/ucdavis-bioinformatics/sickle) | not in MSI | [X] [ ] | | Fast STRUCTURE | 1.0 | Not in MSI | 1.0 | [Fast Structure](https://rajanil.github.io/fastStructure/) | none | [X] [ ] | | Bedops | 2.4.20 (08-30-16) | Not in MSI | 2.4.20 (07-27-16) | [Bedops](http://bedops.readthedocs.io/en/latest/index.html#) | None | [X] [ ] | | Morrell Lab ANGSD-Wrapper Archive | N/A | not in MSI | removed from lab | no URL | not in MSI | N/A |
