Downloads

The latest version of LR_Gapcloser, including the download.

Case 1: Closing Human CHM1htert genome

The H. sapiens gap closure files in our manuscript could be downloaded below, including:

1.1 genome data Source
H. sapiens initial genome contigs:human.quiver.ctg.fasta;

1.2 corrected PacBio reads Source
H. sapiens corrected PacBio reads:polished sequences

1.3 How to evaluate the accuracy of assembly?
We selected the closed reference gaps and re-aligned them to their corresponding sequences using BLAT and BLASTN. The accuracy was measured using the alignment identity. The identity was the ratio of match base number to the reference gap length. The higher the alignment identity, the better the gap-closure performance.

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

1.5 Final gap closure files in the comparison
H. sapiens initial genome contigs: human_contig.tar.gz;
H. sapiens simulative genome with gap:
100 gaps: 100_human_gap_genome.fasta; 30000 gaps:30000_human_gap_genome.fasta
H. sapiens genome gap closed using PBjelly with corrected PacBio reads: Human-100-PBjelly-gapclosed.fasta
H. sapiens genome gap closed using GMcloser with corrected PacBio reads: Human-100-GMcloser-gapclosed.fasta
H. sapiens genome gap closed using LR_Gapcloser with corrected PacBio reads: Human-100-LRGcloser-gapclosed.fasta

Case 2: Closing E. coli K12 MG1655 genome

The E. coli gap closure files in our manuscript could be downloaded below, including::

2.1 genome data Source
E. coli initial genome contigs: ecoli.quiver.all.fasta

2.2 corrected PacBio reads Source
E.coli corrected PacBio reads:polished sequences

2.3 Final gap closure files in the comparison
E. coli simulative genome with gap: 100_ecoli_gap_genome.fasta
E. coli genome gap closed using PBjelly with corrected PacBio reads: Ecoli-PBjelly-gapclosed.fasta
E. coli genome gap closed using GMcloser with corrected PacBio reads: Ecoli-GMcloser-gapclosed.fasta
E. coli genome gap closed using LR_Gapcloser with corrected PacBio reads: Ecoli-LRGcloser-gapclosed.fasta

Case 3: Closing S. cerevisiae W303 genome

The S. cerevisiae gap closure files in our manuscript could be downloaded below, including:

3.1 genome data Source
S. cerevisiae initial genome contigs: yeast.quiver.ctg.fasta.gz

3.2 corrected PacBio reads Source
S. cerevisiae corrected PacBio reads: polished sequences

3.3 Final gap closure files in the comparison
S. cerevisiae simulative genome with gap: 514_yeast_genome.fasta
S. cerevisiae genome gap closed using PBjelly with corrected PacBio reads: Yeast-PBjelly-gapclosed.fasta
S. cerevisiae genome gap closed using GMcloser with corrected PacBio reads: Yeast-GMcloser-gapclosed.fasta
S. cerevisiae genome gap closed using LR_Gapcloser with corrected PacBio reads: Yeast-LRGcloser-gapclosed.fasta

Case 4: Closing A. thaliana Ler-0 genome

The A. thaliana gap closure files in our manuscript could be downloaded below, including:

4.1 genome data Source
A. thaliana initial genome contigs: athal.quiver.ctg.fasta.gz

4.2 corrected PacBio reads Source
A. thaliana corrected PacBio reads: athal.polished.fastq.gz

4.3 Final gap closure files in the comparison
A. thaliana simulative genome with gap: 5000_athal_gap_genome.fasta
A. thaliana genome gap closed using PBjelly with corrected PacBio reads: Athal-PBjelly-gapclosed.fasta
A. thaliana genome gap closed using GMcloser with corrected PacBio reads: Athal-GMcloser-gapclosed.fasta
A. thaliana genome gap closed using LR_Gapcloser with corrected PacBio reads: Athal-LRGcloser-gapclosed.fasta

Case 5: Closing D. melanogaster ISO1 genome

The D. melanogaster gap closure files in our manuscript could be downloaded below, including:

5.1 genome data Source
D. melanogaster initial genome contigs: contigs.tar.gz

5.2 corrected PacBio reads Source
D. melanogaster corrected PacBio reads: polished sequences

5.3 Final gap closure files in the comparison
D. melanogaster simulative genome with gap: 5000_dmel_gap_genome.fasta
D. melanogaster genome gap closed using PBjelly with corrected PacBio reads: Dmel-PBjelly-gapclosed.fasta
D. melanogaster genome gap closed using GMcloser with corrected PacBio reads: Dmel-GMcloser-gapclosed.fasta
D. melanogaster genome gap closed using LR_Gapcloser with corrected PacBio reads: Dmel-LRGcloser-gapclosed.fasta

Case 6: Closing different species genome with different depth of corrected PacBio reads by LR_Gapcloser
H. sapiens genome gap closed using LR_Gapcloser with different depth of corrected PacBio reads: depth_Yeast
E. coli genome gap closed using LR_Gapcloser with different depth of corrected PacBio reads: depth_Ecoli
S. cerevisiae genome gap closed using LR_Gapcloser with different depth of corrected PacBio reads: depth_Yeast
A. thaliana genome gap closed using LR_Gapcloser with different depth of corrected PacBio reads: depth_Athal
D. melanogaster genome gap closed using LR_Gapcloser with different depth of corrected PacBio reads: depth_Dmel

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