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Case 1: Scaffolding human genome

1.1 genome data Source

The human assembly files in our manuscript could be downloaded below, including:
complete genome of hg38: hg38.tar.gz;
human initial genome contigs: contigs.tar.gz;

Different sources of RNA-seq reads used in scaffolding include:

1.2 RNA-seq Source Library 1: Illumina RNA-seq reads in Brain
ERR420392, ERR420391, ERR420386, ERR420387
Library 2: Illumina RNA-seq reads in Liver
ERR420389, ERR420393, ERR420390, ERR420388,
Library 3: Illumina RNA-seq reads in Lung
SRR1297303, SRR1297304, SRR1297305, SRR1297306,
Library 4: Illumina RNA-seq reads in multiple cells
PRJNA292498

1.3 How to evaluate the accuracy of assembly?
Using the order and orientation of contigs on the hg38 assembly as the golden standard (available here ), we estimated the correct links scaffolded and calculated the proportion of corrected links out of all links.

1.4 What scaffolders are used in the comparison?
(1). BESST_RNA;
(2). AGOUTI;
(3). Rascaf;
(4). RNAPATH;
(5). L_RNA_scaffolder;

1.5 Final assembly files in the comparison

human complete genome of hg38 : hg38.tar.gz;
human initial genome contigs: human_contig.tar.gz;
human genome scaffolded using BESST_RNA with human Brain RNA-seq reads: brain_BESST_RNA.fasta; ( BESST_RNA connections )
human genome scaffolded using AGOUTI with human Brain RNA-seq reads: brain_AGOUTI.fasta; ( AGOUTI connections )
human genome scaffolded using Rascaf with human Brain RNA-seq reads: brain_Rascaf.fasta; ( Rascaf connections )
human genome scaffolded using RNAPATH with human Brain RNA-seq reads: brain_RNAPATH.fasta; ( RNAPATH connections )
human genome scaffolded using L_RNA_scaffolder with human Brain RNA-seq reads: brain_L_RNA_scaffolder.fasta; ( L_RNA_scaffolder connections )
human genome scaffolded using P_RNA_scaffolder with human Brain RNA-seq reads: brain_P_RNA_scaffolder.fasta; ( P_RNA_scaffolder connections )

If you have any trouble using P_RNA_scaffolder, then please first follow the steps in our Documentation before contacting us.

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