Contents
What kind of alignment program is HISAT2?
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
How is HISAT2 used in next generation sequencing?
HISAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Based on an extension of BWT for graphs ( Sirén et al. 2014 ), we designed and implemented a graph FM index
How big is HISAT2 compared to the human genome?
HISAT2’s index size for the human reference genome and 12.3 million common SNPs is 6.2GB (the memory footprint of HISAT2 is 6.7GB). The SNPs consist of 11 million single nucleotide polymorphisms, 728,000 deletions, and 555,000 insertions. The insertions and deletions used in this index are small (usually <20bp).
What’s the difference between HISAT2 and TopHat2?
When using graph-based indexes (HGFM), the runtime of HISAT2 is slightly slower than HISAT (30~80% additional CPU time). HISAT2 allows for mapping reads directly against transcripts, similar to that of TopHat2 (use genome_tran or genome_snp_tran ).
What does qualimap do for sequencing alignment data?
Qualimap examines sequencing alignment data in SAM/BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.
What is qualimap 2 and what does it do?
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.