Resources

Genome assembly

• Flye genome assembler

• canu: [10.1101/gr.215087.116]

• BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs [10.1093/bioinformatics/btv351 ]

• quast: qualify assessment tools for genome assemblies [10.1093/bioinformatics/btt086 ]

Long-read transcriptome

• deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index []

scRNA-seq - cluster annotation

• Garnett: automatic cell type classification

scRNA-seq - trajectory inference

• Slingshot: trajectory inference for single-cell data

• scVelo: RNA velocity generalized through dynamical modeling

• CellRank: directed single-cell fate mapping