Tool and Paper Watch

Welcome back! Here I have decided to update the tools available for each of the sections:
Genomics; Transcriptomics; Databases; Statistics; Data analysis:

Genomics:
Assembly:

Annotation: Updating and improving genome annotation: https://academic.oup.com/nar/article/47/2/559/5213907
Comparative Genomics: https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15687
Genome compartmentalization: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824034/


Transcriptomics:
Analysis:
1. DEE2: Digital Expression Explorer 2: Is a database containing analyzed RNAseq data from multiple platforms: http://dee2.io/about.html
2. RNAseqAnalysis pipeline and resources: https://github.com/crazyhottommy/RNA-seq-analysis#databases
3. Best Practises for detecting germline variations in human genomes; https://www.nature.com/articles/s41587-019-0054-x
4. Deep learning with empirical RNAseq evidence (DART) : https://github.com/Xinglab/DARTS
https://www.nature.com/articles/s41592-019-0351-9

Metagenome assemblies
https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbz025/5371422

Databases:


Statistics & R:
Cola: A General Framework for Consensus and Hierarchical partitioning: https://github.com/jokergoo/cola