Results for "Picard"
Blogs
BBTools for bioinformatician !
...rk/remove sequence duplicates (optical/PCR/otherwise) from NGS data This does NOT require alignments so it should prove more useful compared to Picard MarkDuplicates. Relevant opti...2264 days ago
Illumina based assembly pipeline steps !
...(Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (picard; optional) Alignment-level QC (picard, SAMtools) Genome-wide and a...871 days ago
Bookmarks
- Picard is a set of command line tools for manipulating high-throughput sequencing (HT...uctions and implementation/development resources are available on GitHub. The Picard toolkit is open-source under...
2922 days ago
Best Practices for Variant Calling with the GATK
...Video 03/19/15 Introduction to the GATK Geraldine Van der Auwera PDF Video 03/19/15 Mapping, processing, and duplicate marking with Picard tools Matt Sooknah PDF Vid...1528 days ago
Top-level pages
List of Bioinformatics Software Tools for Next Generation Sequencing
...ling from normal-tumor pair and two parent genomes; quantifies descent-by-modification relationships; Written in Java Input: BAM files (parsed by Picard/Samtools API) Reference Geno...2902 days ago
- alignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to se...
2863 days ago
- +1 more Top-level pages
Wire posts
Bio-Scripts
- ...ters CheckIlluminaDirectory (Picard) Asserts the val...ollectIlluminaBasecallingMetrics (Picard) Collects Illumina Basecall...pileup CheckTerminatorBlock (Picard) Asserts the p...ts reads by name FastqToSam (Picard) Con...
2069 days ago
Bash script to alignment of short reads against reference genome !
...marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same criteria for marking duplicates as picard. minimap2 -ax sr -t 40 -R...1553 days ago
- +4 more Bio-Scripts
