All Questions
8
questions
2
votes
2
answers
68
views
Longstitch error make: command: Command not found *** No rule to make target
I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
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- 21
1
vote
0
answers
97
views
RagTag patch error--"Tuple index out of range"
This question was also asked on GitHub
I'm trying to correct a long-read assembly with a short-read scaffold; I'm hoping to fill in the short gaps in the scaffold with the matching long-read sections. ...
- 31
1
vote
1
answer
88
views
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
0
votes
1
answer
137
views
Resources to learn genome assembly workflow for small genomes (like viruses)
I have sequencing data of a few samples of a DNA virus.
I'd like to learn de novo assembly of 'short read' data, to construct a scaffold and then count the abundance of each strain in the data.
I ...
- 169
3
votes
2
answers
788
views
Is there any value in scaffolding the output contigs of MEGAHIT assembler given a metagenomic dataset?
As far as I understood, for most assembly programs, the scaffolding step takes into consideration paired-end information in order to get from contigs (contiguous sequences) to scaffolds (longer ...
- 1,007
3
votes
1
answer
141
views
Scaffolding a genome with hybrid data
I am assembling a ~500MB genome, and have ~150x long reads and ~200x 150bp PE short reads, with a ~400bp insert size.
I've done a lot of work with minimap+miniasm, and have what I think is a good set ...
- 972
4
votes
2
answers
439
views
Reordering scaffolds according to a reference without a genetic map
I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
- 325
5
votes
1
answer
335
views
What causes the difference in total length of assembled contigs and scaffolds in SOAPdenovo2?
I use SOAPdenovo2 to assemble a large genome (4.8G) using ~20X paired-end reads. The total length of contig sizes is 6.3G while total length of scaffolds is 2.7G. Note that this is a haploid genome, ...
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