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...2270 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...876 days ago
2927 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...1533 days ago
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...2908 days ago
2868 days ago
2074 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...1558 days ago