CEES bioinformatics knowledge

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

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

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

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