Difference between revisions of "CEES bioinformatics knowledge"
From mn/bio/cees-bioinf
| Line 13: | Line 13: | ||
| 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 | + | | R-statistics, some python, Unix |
|- | |- | ||
| Anna Mazzarella | | Anna Mazzarella | ||
| 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 |
|- | |- | ||
| 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 | ||
| + | | | ||
| | | | ||
|} | |} | ||
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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> |
| + | |||
| + | <br> | ||
| + | |||
| + | <br> | ||
| + | |||
| + | <br> , | ||
Revision as of 13:23, 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 |
If you want your knowledge to be added to the list,
please send an e-mail to: genomic-analyses at ibv.uio.no
,
