Difference between revisions of "CEES bioinformatics knowledge"
From mn/bio/cees-bioinf
| Line 18: | Line 18: | ||
| Stickleback | | Stickleback | ||
| Rad tag sequencing, mapping, simple bash scripting | | Rad tag sequencing, mapping, simple bash scripting | ||
| − | | Stacks, bowtie, bwa, samtools, gmap, gsnap | + | | Stacks, bowtie, bwa, samtools, gmap, gsnap |
| | | | ||
|- | |- | ||
| Tore Oldeide Elgvin | | Tore Oldeide Elgvin | ||
| Sparrows | | Sparrows | ||
| − | | WGS Illumina data, assembly, assembly validation, mapping, population genomics | + | | WGS Illumina data, assembly, assembly validation, mapping, population genomics |
| − | | MEGA, Arlequin, DNAsp, Geneious, Reapr, CEGMA, Allpaths-LG, samtools, bwa | + | | MEGA, Arlequin, DNAsp, Geneious, Reapr, CEGMA, Allpaths-LG, samtools, bwa |
| basic unix | | basic unix | ||
|- | |- | ||
| Line 30: | Line 30: | ||
| 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, PacBio's smrtanalysis | + | | Various assemblers, BWA, samtools, PacBio's smrtanalysis |
| unix, sed, awk, python, perl | | unix, sed, awk, python, perl | ||
|- | |- | ||
| − | | Monica H. Solbakken | + | | Monica H. Solbakken |
| − | | Atlantic cod | + | | Atlantic cod |
| − | | De novo transcriptome assembly, mapping, differential expression, genome mining. HiSeq and 454 data mainly | + | | 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 | + | | Trinity, bwa, bowtie, blastx annotation pipeline, other misc software on the cod nodes, edgeR, DEseq |
| | | | ||
|- | |- | ||
| − | | Ole Kristian Tørresen | + | | Ole Kristian Tørresen |
| − | | Atlantic cod and other teleosts | + | | Atlantic cod and other teleosts |
| − | | De novo assembly, mapping, sequencing strategies, sequencing technologies, quality control Assemblers (most of them), bwa, samtools | + | | De novo assembly, mapping, sequencing strategies, sequencing technologies, quality control |
| − | | some R, some python | + | | Assemblers (most of them), bwa, samtools |
| − | + | | some R, some python | |
|- | |- | ||
| − | | Stephanie Hänsch | + | | Stephanie Hänsch |
| − | | ancient DNA | + | | ancient DNA |
| − | | Aligning with samtools, Sequence trimming with dedicated scripts, MEGAN, blast | + | | 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, | If you want your knowledge to be added to the list, | ||
| − | please send an e-mail to: genomic-analyses at ibv.uio.no<br> | + | please send an e-mail to: genomic-analyses at ibv.uio.no<br> |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 13:49, 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, 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
