Results for "FastQC"
Blogs
Protocol for De novo Genome Assembly using Illumina Reads
...efficiency of the assembly. Read Quality Control:Check the qualiy with fastQC.Scripthttps://bioinformaticsonline.com/snippets/view/42540/install-fastqc-using-conda Quality trimming...1188 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) S...861 days ago
Bookmarks
- ...content per sequence GC content per sequence quality sequence length distribution More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/...
2926 days ago
- ...ploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is...
2801 days ago
- +3 more Bookmarks
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...s a reference sequence] Quake: quality-aware detection and correction of sequencing errors. Kelley et al, Genome Biol 11(11):R116, 2010. PubMed FastQC: a quality control tool for h...3763 days ago
- ...ing linux command from within python code Example: if you want to run fastqc for QC of fastq file: from subprocess import Popen,PIPE,call p=Popen(["fastqc","-f","fastq","-o", "/home/na...
3533 days ago
Wire posts
Opportunity posts
- ...ng: Programming: Perl and Python. Operating system: Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cuf...
3149 days ago
Bio-Scripts
- (JitMetaENV) ➜ JitMeta conda install -c bioconda fastqc Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1200 days ago
Tags
- Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. Note that the information on this pag...
Tags: Bioinformatics, NGS, Assembly, BAM, SAM, CRAM, Picard, FastQC, Tool, Software
2912 days ago
- Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at http://www.bioinformatics.babraham.ac.uk/projec...
Tags: Bioinformatics, NGS, Assembly, Quality, FastQC, Tutorial
2926 days ago
- +1 more Tags
Comments
Comment on "Short-read assembly using Spades !"
...e of high quality and do not contain sequencing errors or low-quality bases. This step can be performed using various tools such as Trimmomatic or FastQC. Running SPAdes: After q...399 days ago
- ...n rates dependent on the expression levels. FastQC FastQC is a quality control too...esented in HTML permanent reports. FastQC can be run as a stand-alone a...visualise results from numerous tools (FastQC, HTSeq, RSeQC, Tophat, STAR,...
2121 days ago
