Difference between revisions of "CEES bioinformatics knowledge"
From mn/bio/cees-bioinf
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A non-extensive list of CEES participants and their knowledge on bioinformatics and various software tools<br> | A non-extensive list of CEES participants and their knowledge on bioinformatics and various software tools<br> | ||
| − | {| width=" | + | {| width="800" cellspacing="1" cellpadding="1" border="0" align="Center" |
|- | |- | ||
| Name | | Name | ||
| Project | | Project | ||
| Knows about | | Knows about | ||
| − | | Experience with software | + | | Experience with software |
| + | | programming language | ||
|- | |- | ||
| Thomas Haverkamp | | Thomas Haverkamp | ||
| Thermotoga genomes | | Thermotoga genomes | ||
| Genome assembly, Mapping, Sequence Quality control, shot-gun seq, amplicon sequencing, Pacbio data, MiSeq data, Sequence classification, slurm jobs | | 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 | + | | Various assemblers (e.g: Velvet, SPAdes, SGA), Bwa, samtools, Mothur, MEGAN, comparative genomics |
| + | | R-statistics, a tiny bit of python | ||
|- | |- | ||
| Anna Mazzarella | | Anna Mazzarella | ||
| Line 25: | Line 27: | ||
| Lex Nederbragt | | Lex Nederbragt | ||
| Atlantic cod, Norwegian Sequencing Centre | | 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 | + | | 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, unix, sed, awk, python, perl, PacBio's smrtanalysis | | Various assemblers, BWA, samtools, unix, sed, awk, python, perl, PacBio's smrtanalysis | ||
|} | |} | ||
Revision as of 13:12, 24 February 2014
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, a tiny bit of python |
| 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, basic unix | MEGA, Arlequin, DNAsp, Geneious, Reapr, CEGMA, Allpaths-LG, samtools, bwa | |
| 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, unix, sed, awk, python, perl, PacBio's smrtanalysis |
If you want your knowledge to be added to the list,
please send an e-mail to: genomic-analyses at ibv.uio.no
