All Questions
Tagged with assembly reference-genome
9
questions
1
vote
1
answer
61
views
How to subset an SRA file for a single chromosome?
I used prefetch to get the Pacbio reads of chicken from the SRA database. I want to align these reads against a reference genome, but not all the reads. I am only interested in a particular region on ...
- 105
0
votes
0
answers
222
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How to manually curate a genome assembly for sequence variation or error?
I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, ...
- 75
0
votes
1
answer
74
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How to improve a genome assembly using Dovetail and PacBio assembly?
I have more of a conceptual question. I have two genome assemblies from the same plant, one from Dovetail technology (~998 Gb) and another is PacBio HiFi assembly (~1.1 Gb). The Dovetail assembly is ...
- 75
1
vote
1
answer
88
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Which one is a more convenient assembly?
I have developed a software for de novo genome assembly. Its performance varies gradually according to how much data you employ. At initial stages it often produces contigs that look like that when ...
- 359
1
vote
1
answer
188
views
Interpreting contig alignments to a reference genome
I have applied two de novo genome assembly tools to data from the run SRR12707453, corresponding to a phage (I downloaded the data and have no relation with the authors of the study).
Using rnaSPAdes ...
- 359
1
vote
2
answers
212
views
How can I get or create a reference genome for Bacteria?
I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant ...
- 13
1
vote
1
answer
106
views
Gap-fill assembly with PacBio reads
I would like to gap-fill (or correct) a mammalian-sized assembly for which we have BACs that have been sequenced with PacBio CLR data. I have seen there are pbm22/gcpp tools available for correcting ...
- 2,344
0
votes
1
answer
208
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Does the galGal5 chicken assembly have a chromosome 29?
The chromosome sizes at UCSC don't seem to contain chr29:
ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.chrom.sizes
It has a chr28 and a chr30. Am I missing something or is there ...
- 910
2
votes
2
answers
729
views
Java error when launching Pilon
I am trying to use Pilon to improve a reference based on some Illumina data I have got. So, I aligned the Illumina reads to the reference using bwa. Then, I want to use Pilon to improve the reference ...
- 2,469