Downloads

The latest version of LR_Gapcloser, including the download.

Case 1: Closing the gaps in S. cerevisiae S288C genome

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

1 Long reads Source
Yeast-Corrected-Pacbio.fa.gz
Yeast-Uncorrected-Pacbio.fa.gz
Yeast-Corrected-Nanopore.fa.gz
Yeast-Uncorrected-Nanopore.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 with uncorrected Pacbio reads
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 NGS-derived assemblies with corrected Pacbio reads
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 Gap closure on NGS-derived assemblies with uncorrected Nanopore reads
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

4.4 Gap closure on NGS-derived assemblies with corrected Nanopore reads
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

4.5 Gap closure on Repeat-derived assemblies with uncorrected Pacbio reads
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

4.6 Gap closure on Repeat-derived assemblies with corrected Pacbio reads
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

4.7 Gap closure on Repeat-derived assemblies with uncorrected Nanopore reads
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

4.8 Gap closure on Repeat-derived assemblies with corrected Nanopore reads
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

4.9 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 the gaps in C. elegans Bristol genome

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

1 Long reads source
Celegans-Uncorrected-Pacbio.fa.gz
Celegans-Corrected-Pacbio.fa.gz
Celegans-Uncorrected-Nanopore.fa.gz
Celegans-Corrected-Nanopore.fa.gz

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

3.1 Gap closure on NGS-derived assemblies with uncorrected Pacbio reads
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 NGS-derived assemblies with corrected Pacbio reads
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 NGS-derived assemblies with uncorrected Nanopore reads
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 Gap closure on NGS-derived assemblies with corrected Nanopore reads
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

3.5 Gap closure on Repeat-derived assemblies with uncorrected Pacbio reads
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

3.6 Gap closure on Repeat-derived assemblies with corrected Pacbio reads
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

3.7 Gap closure on Repeat-derived assemblies with uncorrected Nanopore reads
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

3.8 Gap closure on Repeat-derived assemblies with corrected Nanopore reads
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

3.9 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 the gaps in the Human CHM1 chrX genome

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

1 Long reads source
human.polished.fastq.bz2
the corrected Pacbio reads from chromosome X is available at chrX-Corrected-Pacbio.fastq.gz
the uncorrected Pacbio reads from chromosome X is available at chrX-Uncorrected-Pacbio.fa.gz

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

3.1 Gap closure on NGS-derived assemblies with uncorrected Pacbio reads
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 NGS-derived assemblies with corrected Pacbio reads
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 Repeat-derived assemblies with uncorrected Pacbio reads
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

3.4 Gap closure on Repeat-derived assemblies with corrected Pacbio reads
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

3.5 Gap closure on real gaps on chromosome X with uncorrected Pacbio reads
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

3.6 Gap closure on real gaps on chromosome X with corrected Pacbio reads
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

3.7 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

Case 4: Closing the gaps in the largest scaffold (KQ079791) from Human GM12878 genome

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

1 Long reads source
the uncorrected Nanopore reads from this scaffold is available KQ079791.Uncorrected_Nanopore.fasta.gz
the corrected Nanopore reads from this scaffold is available KQ079791.Corrected_Nanopore.fasta.gz

2 KQ079791 sequence
KQ079791.fa.gz

3.1 Gap closure on real gaps in KQ079791 with uncorrected Nanopore reads
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 real gaps in KQ079791 with corrected Nanopore reads
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

Case 5: Updating the large and complex genome assemblies

1 Updated three high-quality human 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

2 Updated wheat A genome assemblies
Wheat A genome assembly with gaps closed using LR_Gapcloser Update-wheatA.fasta.gz

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

Comments are closed.