File	README.md
Lecture	Advanced Bioinformatics 1
Professor	Martin Steinegger (martin.steinegger@snu.ac.kr)
TA	Hyunbin Kim (khb7840@snu.ac.kr)
Last Modified	2021-09-01 06:14:16 -0700

Advanced Bioinformatics 1

The paper pool for Advanced Bioinformatics 2021

Annotation

1. Prokka paper, github
2. Augustus paper, github
3. Maker paper, homepage
4. Prodigal paper, github

Genome comparison

1. mummer1-4 paper, github
2. mash paper, github

Multiple sequence alignment (MSA)

1. clustalomega paper, github, homepage
2. mafft paper, github, homepage
3. muscle paper1, paper2, github, homepage

Homology search

1. mmseqs2 paper, github
2. Diamond1+2 paper1, paper2, github
3. HHblits paper, github

Transcript

1. stringtie1+2 paper1, paper2, github, homepage
2. kallisto paper, github, homepage
3. salmon paper, github, homepage

Metagenomics

1. metaphlan2 metaphlan1_paper, metaphlan2_paper, github, homepage
2. kraken-uniq paper, github
3. kraken2 paper, github
4. HUMAnN2 paper, github, homepage

Phylogenetics

1. raxml paper, github, homepage
2. fasttree paper1,paper2, homepage
3. iqtree paper, github, homepage

RNA structure prediction

1. viennarna paper, github, homepage
2. Geometric deep learning of RNA structure paper, zenodo1, zenodo2, zenodo3

Protein structure

1. AlphaFold2 paper, github
2. RoseTTAFold paper, github
3. gromacs paper, github, homepage

Workflow and package

1. nextflow paper, github, homepage
2. snakemake paper, github, documentation
3. bioconda paper, github
4. bioconductor paper1, paper2, github, homepage

Assembler

1. spades paper, github, homepage
2. trinity paper, github
3. flye paper, github
4. hifiasm paper, github

Read aligner

1. hisat1+2 paper, github, homepage
2. star paper, github
3. minimap2 paper, github
4. vsearch paper, github

Language models

1. ProtTrans paper, github
2. ESM paper, github
3. DNABERT paper, github

Variant caller

1. freebayes paper, github
2. pilon paper, github
3. gatk paper1, paper2, github, homepage

Other topics

1. Conterminator paper, github
2. VG paper, github