Difference between revisions of "CEES bioinformatics knowledge"
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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, some python, Unix | ||
|- | |- | ||
| Anna Mazzarella | | Anna Mazzarella | ||
Line 17: | Line 19: | ||
| 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 | ||
|- | |- | ||
| 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, | + | | 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) | ||
|} | |} | ||
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