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Datové struktury, algoritmy
a nástroje pro zpracování
genomických dat
IV110/IV114/E4014 Projekt z bioinformatiky (a systémové biologie)
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NGS sequencing
Read length
Gbp per run
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FASTQ data
format
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Efficient read mapping
algorithms are based
on k-mers
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Suffix trees
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BWT-based index
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Enhanced suffix array and BWT-based indexes
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Read mapping tool
Performance
CPU
RAM
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Assembly
alternatives
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Overlap graph for overlap-layout-consensus assembly
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DeBruijn graph
for assembly
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MAPPING
Bowtie2, STAR, BWA-MEM
ASSEMBLY
SHORT READ
Velvet, AbySS, SOAPdenovo
LONG READ
Flye, Canu, miniasm, Minipolish, NECAT,
NextDeNovo, Nextpolish, Raven, Redbean, Shasta
HYBRID
SPADes, MaSuRCA, Unicycler
Tools for NGS
Read processing
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Nanopore read
Processing pipeline
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Command-line examples
for various nanopore
assembly tools
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Contig N50
COMPASS
BUSCO score
LAI score
Genome assembly
quality assessment
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3rd
gen-seq
tools
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JBrowse
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JBrowse
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JBrowse