Long-reads de novo assembly benchmarking
This page gathers the input/output data and scripts used for our de novo assembly benchmarking analysis. inputs consist of 5 datasets :
- LSK114_SIRV_cDNA
- LSK114_chrIS_mixA_cDNA
- LSK109_chrIS_mixA_cDNA
- RNA002_chrIS_mixA_dRNA
- RNA004_chrIS_mixA_dRNA
See Figure1 for more information about this analysis.
- Tools-guide.txt = Installation guidelines and how tools were executed.
- Assembly-pipeline.sh = Commandlines executed for each of the tools tested (except Bambu which runs on R --> see Bambu-time.R instead).
- Bambu-time.R = code to execute Bambu and Bambu-noRef for one sample.
Input .fastq files as used in this study for SIRV and sequin data are available on ENA (European Nucleotide Archive) [PRJEB74162]
Authorship : Anshul Budhraja ; Mélanie Sagniez ; Martin Smith