simplesetr.blogg.se - File time come out from next generation sequencing sam

#File time come out from next generation sequencing sam mac os
#File time come out from next generation sequencing sam software
#File time come out from next generation sequencing sam torrent

#File time come out from next generation sequencing sam mac os

Available on Windows, Mac OS X, Linux, and the Amazon Cloud.

Supports all major NGS technologies (Illumina, Ion Torrent, Pac Bio and Roche 454) and project types.

Annotates genomic data with allele and genotype frequency, functional impact predictions, evolutionary conservation scores and pathogenicity.

Aligns exome data and performs variant calling an average of 3 times faster than alternative pipelines.

#1 in accuracy: fewer false negatives and better sensitivity compared to results obtained from other aligners.

Supported workflows include: reference-guided and de novo genome and transcriptome assembly and analysis, metagenomics sample assembly, targeted resequencing, exome alignment, gene panels with validation control, variant analysis, and RNA-Seq, ChIP-Seq and miRNA alignment and analysis.

#File time come out from next generation sequencing sam software

Comprehensive NGS software pipeline for assembly, alignment, variant calling and analysis of NGS data.

Has own database- “knowledge base” based on COSMIC, OMIM, and TCGA databases.

(QIAGEN) allows for variant identification and analysis, uses NCI-60 data set for cancer, Supported third part informatin: Entrez Gene, RefSeq, ClinVar gives contextual details of results instead of just A to B relationship.Private cloud repository - formerly a redistributor of SRA and other NCBI resources command-line or via web, can fetch data from a URL, build custom pipeline/ workflow has site: data downloads come directly from NCBI.

#File time come out from next generation sequencing sam torrent

De novo assembly: “In addition to Sanger sequence data, reads from these high-throughput sequencing machines are supported The 454 FLX System and the 454 GS Junior System from Roche, Illumina Genome Analyzer, Illumina HiSeq, Illumina HiScan, and Illumina MiSeq sequencing systems, SOLiD system from Life Technologies, Ion Torrent system from Life Technologies”.Read mapping: “In addition to Sanger sequence data, reads from these high-throughput sequencing machines are supported: The 454 FLX System and the 454 GS Junior System from Roche, Illumina Genome Analyzer, Illumina HiSeq, Illumina HiScan, and Illumina MiSeq sequencing systems, SOLiD system from Life Technologies, Ion Torrent system from Life Technologies, Helicos from Helicos BioSciences”.Also accepts: FASTA, GFF/GTF/GVF, BED, Wiggle, Cosmic, UCSC variant database, complete genomics master var file.Accepts VCF files from 1000 Genomes Project.Features include: resequencing, workflow, read mapping, de novo assembly, variant detection, RNA-Seq, ChIP-Seq, Genome Browser, etc (entire list on website) Main Workbench offers database search (Genbank, Blast, Pubmed) 2000 organizations have invested in CLC DNA-Seq Feature, can annotate with dbSNP.Alignment feature: Supports alignment from Illumina, Ion Torrent, 454 (Roche), and Pac Bio.

In addition, prealigned data in SAM, BAM or Illumina-specific ELAND format can be directly imported for analysis.” Supports workflows “one can import the sample data in FASTA, FASTQ or tag-count format. offers many different tools including alignment, RNA-Seq, DNA-Seq, ChIP-Seq, Small RNA-Seq, Genome Browser, visualizations, Biological Interpretation, etc.