Kalkyl

From SNIC Documentation

Jump to: navigation, search
Name Kalkyl
Description cluster resource of about 21 TFLOPS
Resource type compute
Centre UPPMAX
Is active no
Start date 2010-03-01
End date   2014-01-01

Available software

Software Field License Description
ABySS Bioinformatics Free A parallel assembler for short read sequence data
ANFO Bioinformatics Free A parallel assembler for short read sequence data
ANNOVAR Bioinformatics Free Functional annotation of genetic variants from high-throughput sequencing data
Ab wtp Bioinformatics Free Alignment tool for SOLiD transcript reads
BEDTools Bioinformatics Free BEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLAST Bioinformatics Free package for aligning nucleotide or amino acid sequences
BLAT Bioinformatics Free an alignment tool like BLAST, but it is structured differently.
BWA Bioinformatics Free A fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverter Bioinformatics Free Converts bcl files to Qseq files.
BioPerl Bioinformatics Free A community effort to produce Perl code which is useful in biology.
BioPython Bioinformatics Free A set of freely available tools for biological computation written in Python by an international team of developers.
Bioscope Bioinformatics Site license the pipeline stack that comes with the solid sequence platform
Bowtie Bioinformatics Free Bowtie is an ultrafast, memory-efficient short read aligner.
CASAVA Bioinformatics Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software
Concaterpillar Bioinformatics Free A hierarchical likelihood ratio test for phylogenetic congruence.
Cufflinks Bioinformatics Free Assembles transcripts in RNA-Seq samples and calculates their abundances
EMBOSS Bioinformatics Free A free Open Source software analysis package developed for the molecular biology.
EMMAX Bioinformatics A statistical test for large scale human or model organism association mapping accounting for the sample structure.
FASTX Bioinformatics Free A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
FastQC Bioinformatics Free Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
FreeBayes Bioinformatics Bayesian SNP and short indel caller from the Marth lab (who created Mosaik).
GAMESS Computational materials science
Computational chemistry
Free ab initio quantum chemistry
GARLI Bioinformatics Performs heuristic phylogenetic searches ...
GATK Bioinformatics Free Structured software library for writing analysis tools for next-generation sequencing data.
GCTA Bioinformatics A tool for Genome-wide Complex Trait Analysis
Gaussian Computational chemistry Site license widely used quantum chemistry software
GenomeTools
HMMER Bioinformatics Free package for working with profile hidden Markov models (HMM)
MIRA
MOSAIK
MUMmer
Maq
Matrix2png
Mpiblast
MrBayes Bioinformatics Free Bayesian estimation of phylogeny
Picard
RAxML
Ray
SAMtools
SOAPdenovo
SolexaQA
SplitSeek
Staden
Tophat
UNAFold
Velvet
Personal tools
Namespaces
Variants
Actions
People
For Staff
Toolbox