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The latest version of LR_Gapcloser, including the download.

Previous version :
LR_Gapcloser_v0.1

Case 1: Closing S. cerevisiae S288C genome

The S. cerevisiae S288C reads and assemblies in our manuscript could be downloaded below, including:

1 corrected PacBio reads Source
Yeast-Corrected-Pacbio.fa.gz

2 How to evaluate the accuracy of assembly?
We used Quast to evaluate the accuracy of each assembly by comparison to the reference genome GCF_000146045.2_R64_genomic.fna.gz.

3 What scaffolders are used in the comparison?
(1). PBjelly;
(2). GMcloser;
(3). LR_Gapcloser;

4.1 Gap closure on NGS-derived assemblies
Initial genome assembly: Pxut_gapClosed.fa.gz;
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

4.2 Gap closure on Repeat-derived assemblies
Initial genome assembly: Repeat-derived.gap.fa.gz;
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

4.3 Assemblies generated by different strategies
Assembly generated by using NGS-based assemblier: Strategy-1.fa.gz
Assembly generated with NGS-based assemblier and then LR_Gapcloser Strategy-2.fa.gz
Assembly generated with TGS-based assemblier Strategy-3.fa.gz
Assembly generated with TGS-based assemblier and then NGS-based assemblier Strategy-4.fa.gz
Assembly generated with TGS-based assemblier and then NGS-based assemblier and finally LR_Gapcloser Strategy-5.fa.gz
Assembly generated with assemblier, which simultaneously supports NGS reads and TGS readsStrategy-6.fa.gz

Case 2: Closing C. elegans Bristol genome

The C. elegans Bristol reads and assemblies in our manuscript could be downloaded below, including::

1 Corrected reads Source
Celegans-Corrected-Pacbio.fa.gz

2 Reference genome and annotation
Assembly GCF_000002985.6_WBcel235_genomic.fna.gz
Annotation GCF_000002985.6_WBcel235_genomic.gff.gz

3.1 Gap closure on NGS-derived assemblies
Initial genome assembly: Pxut_gapClosed.fa.gz;
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

3.2 Gap closure on Repeat-derived assemblies
Initial genome assembly: Repeat-derived.gap.fa.gz;
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

3.3 Assemblies generated by different strategies
Assembly generated by using NGS-based assemblier: Strategy-1.fa.gz
Assembly generated with NGS-based assemblier and then LR_Gapcloser Strategy-2.fa.gz
Assembly generated with TGS-based assemblier Strategy-3.fa.gz
Assembly generated with TGS-based assemblier and then NGS-based assemblier Strategy-4.fa.gz
Assembly generated with TGS-based assemblier and then NGS-based assemblier and finally LR_Gapcloser Strategy-5.fa.gz
Assembly generated with assemblier, which simultaneously supports NGS reads and TGS readsStrategy-6.fa.gz

Case 3: Closing Human CHM1 genome

The Human CHM1 reads and assemblies in our manuscript could be downloaded below, including:

1 Corrected reads Source
human.polished.fastq.bz2
Especially, the corrected Pacbio reads from chromosome X is available chrX-pacbio.fastq.gz

2 Reference chromosome X assembly and annotation
Assembly chrX.fna
Annotation chrX.gff

3.1 Gap closure on NGS-derived assemblies
Initial genome assembly: Pxut_gapClosed.fa.gz;
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

3.2 Gap closure on Repeat-derived assemblies
Initial genome assembly: Repeat-derived.gap.fa.gz;
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

3.3 Gap closure on real gaps on chromosome X
Assembly with gaps closed using PBjelly PBJelly.fa.gz
Assembly with gaps closed using GMcloser GMCloser.fa.gz
Assembly with gaps closed using LR_Gapcloser LR_Gapcloser.fa.gz

3.4 Assemblies generated by different strategies
Assembly generated by using NGS-based assemblier: Strategy-1.fa.gz
Assembly generated with NGS-based assemblier and then LR_Gapcloser Strategy-2.fa.gz
Assembly generated with TGS-based assemblier Strategy-3.fa.gz
Assembly generated with TGS-based assemblier and then NGS-based assemblier Strategy-4.fa.gz
Assembly generated with TGS-based assemblier and then NGS-based assemblier and finally LR_Gapcloser Strategy-5.fa.gz

3.5 Updated three high-quality genome assemblies
Korean genome assembly with gaps closed using LR_Gapcloser Updated.GCA_001750385.2_AK1_v2_genomic.fna.gz
NA12878 genome Assembly with gaps closed using LR_Gapcloser Updated.GCA_001013985.1_ASM101398v1_genomic.fna.gz
CHM1 genome assembly with gaps closed using LR_Gapcloser Updated.CHM1.fa.gz

3.6 Reassemblied CHM1 genome assembly
Assembly Reassembled.CHM1.fa.gz

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