CEES bioinformatics knowledge
From mn/bio/cees-bioinf
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