Results for "NGS READGROUPS GATK FastQ"
Top-level pages
The completion of the first human genome drafts was just a start of the...“high-throughput next generation sequencing” (HT-NGS)...d up the genomic sequencing projects. In the fast growing HT-NGS t...3959 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next generation quantitative...ext Compression of DNA sequence reads in FAST..., Genome Biol 11(11):R116, 2010. PubMed FastQC: a quality control tool for...Eucalyptus. Sansaloni et al., BMC Proceedings 5(Suppl 7):P54, 2011 Full Text...3791 days ago
List of bioinformatics open source projects/software.
Open source software is software that can be freely used, changed,...supports and promotes the open source movement. Followings are the OS bioinformatics proj...tics tools for omics data Genome Analysis Toolkit 1.0 (GATK...3768 days ago
Perl one-liner for bioinformatician !!!
With the emergence of NGS technologies, and sequencing data most of the bio...are several "standardized" file formats (FASTQ, SAM...d they do one thing really well. These things...#converts ascii values into character strings.perl -le '@odd = grep {$_ % 2 =...3639 days ago
Next generation sequencing in R or bioconductor environment
There are many R software and bioconductor packages for NGS data analysis, some of them are as follows Biostrings The Biostrings package from Bioco...s and functions provided by Biostrings form t...rages the biomaRt, IRanges, Biostrings,...e()biocLite(c("ShortRead", "Biostrings",...3636 days ago
Commercial and public next-gen-seq (NGS) software
Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly...r MacOS.Partek - Commercial software for NGS, micro...ib.is library and a set of script targeted to NGS....and and the University of California, BerkeleyNGS-T...3530 days ago
- Subprocess is one of simplest way of running linux co...within python code Example: if you want to run fastqc for QC of fastq file: from subprocess import...me/name/result/","/dev/stdin"],stdin=fopen("read.fastq","r") ,stdout=PIPE,stderr=PIP...
3560 days ago
- Reformat is a member of the BBMap/BBTools...It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (a...ow naming conventions, or out-of-spec fastq files with qualities values l...on. Typical usage examples: Reformat fastq into fasta: reformat.sh in=x....
2725 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...ons: Supports all established NGS sequen...ariants in pool or individual NGS data, reports overall p-value,...PPILP Description: Refines GATK’s Unified Genotyper SNV...daptive multiblups, LD weightings Input: PLINK format Output:.r...Input: Maq, gff, CASAVA, VCF, GATK bed, custom Output: “de...2920 days ago
- alignment: the mapping of a raw sequence read to a l...entire genome for Escherichia coli 536. FAST...d (also known as the Query Name). Used in FASTQ and SAM files. paired-end se...ng quality of base calls, quality of mappings, and probabilities associated w...
2880 days ago
