CEES bioinformatics knowledge

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A non-extensive list of CEES participants and their knowledge on bioinformatics and various software tools

Name Project Knows about Experience with software programming language
Thomas Haverkamp Thermotoga genomes Genome assembly, Mapping, Sequence Quality control, shot-gun seq, amplicon sequencing, Pacbio data, MiSeq data, Sequence classification, slurm jobs Various assemblers (e.g: Velvet, SPAdes, SGA), Bwa, samtools, Mothur, MEGAN, comparative genomics R-statistics, some python, Unix
Anna Mazzarella Stickleback Rad tag sequencing, mapping, simple bash scripting Stacks, bowtie, bwa, samtools, gmap, gsnap
Tore Oldeide Elgvin Sparrows WGS Illumina data, assembly, assembly validation, mapping, population genomics MEGA, Arlequin, DNAsp, Geneious, Reapr, CEGMA, Allpaths-LG, samtools, bwa basic unix
Lex Nederbragt Atlantic cod, Norwegian Sequencing Centre All sequencing platforms, genome assembly, assembly validation and visualisation, reproducible science, version control, good computational practice, using high-performance computing (HPC) infrastructure and the Abel cluster Various assemblers, BWA, samtools, PacBio's smrtanalysis unix, sed, awk, python, perl
Monica H. Solbakken Atlantic cod De novo transcriptome assembly, mapping, differential expression, genome mining. HiSeq and 454 data mainly Trinity, bwa, bowtie, blastx annotation pipeline, other misc software on the cod nodes, edgeR, DEseq
Ole Kristian Tørresen Atlantic cod and other teleosts De novo assembly, mapping, sequencing strategies, sequencing technologies, quality control Assemblers (most of them), bwa, samtools some R, some python
Stephanie Hänsch ancient DNA Aligning with samtools, Sequence trimming with dedicated scripts, MEGAN, blast
Michael Matschiner Teleosts genomes Phylogenetics, genome mining, diversification and trait evolution modelling, mapping, unix, slurm Phylogenetics tools (BEAST, MrBayes, RAxML), Modelling R packages (geiger, OUwie, Motmot, Phytools), Genomic stuff (bwa, samtools, picard-tools, gatk) Ruby (fluent), R, Java, unix (ok-ish), Python, Perl (basic)

If you want your knowledge to be added to the list,

please send an e-mail to: genomic-analyses at ibv.uio.no