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genomics (phylogeny (gene ontologies (annotation (prokka), molecular…
genomics
phylogeny
gene ontologies
annotation (prokka)
molecular function
biological process
cellular component
phylogenies
horizontal inheritance
Recombination
xenology
vertical inheritance
Binary cell division
homology
Kraken
TaxID
coverage checking
read coverage of contigs
de novo
Prokaryotes
transcription
Eukaryote
translation table
DNA sequencing
Instrument
Short read
Illumina
technical error
high GC content
sequence quality {FastQC}
Phred quality score (fastq)
GC content
phasing
crosstalk
short reads
Sanger (low throughput)
Long reads
Nanopore
PacBIo
CANU assembly
PILON correction by Illumina readset
Source of sequence data
Database
INSDC(EMBL-EBI/DDBJ/NCBI)
ENA/DRA/SRA
reference genome
sequence alignment
Edit distance
semi-global
BWA with SAMtools
Local (waterman/FASTA/BLAST)
analysis method
read mapping
variant calling
CNV
LOH
B allele frequency
snippy
VCF
Allele/haplotype
2 more items...
Multiple sequence alignment
MSA
optimise using DPA
STAR
one sequence is considered the ancestor (central sequence)
Progressive
CLUSTALO
T-Coffee
iterative
MUSCLE
Advance assemblies
Metagenomics
amplicon sequencing
PCR
1 more item...
Whole metagenome shotgun sequencing
bacterial community profile
3 more items...
Transcriptome sequencing (RNA-seq)
gene expression
isoforms
alignment file (SAM/BAM)
Database search
BLAST
scoring variation (substitution matrix)
High score pairs
PAM/BLOSUM62
BLASTp
Affine gap cost
mutiple indels
low complexity filtering
SEG for blastp
DUST for blastn
Blastn
E-Value
de novo assembly
assembly software (SPAdes/Megahits)
contig identification
Fasta or Fastq file
Global (DPA/needleman)
similarity to reference genome
Parallel computing