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How can I speed up the assembly for a bacterial genome of 3Mb (which parameters could be modified). I tried with default parameters but it took more than 48h to finish (on Linux computer with 16CPU an…
fetyj updated
6 years ago
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Hi,
I'm a new canu user trying to assemble pacbio reads from bacterial genomes. I followed step-by-step the Installation and Quick Start instructions on the E. coli set but `canu stops at some poin…
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I just gotten a bizarre error with canu1.6 (downloaded from git on Oct17th). It seems canu is unable to detect the read type from my input command?
-nanopore-raw doesn't work either with the raw da…
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Hello, firstly just want to thank you for writing and supporting this assembly software.
We are trying to assemble a heterozygous large genome (1G) using both RSII and Sequel derived sequences. Ou…
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Hello,
I am using Canu for the first time and trying with the quickstart data. I have followed the commands are described in readthedocs but the following is happening:
```
hjb60@hjb60-Virtual-Bo…
hjb60 updated
6 years ago
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I’m trying to use vg for metagenome analysis. As many assembled fragments have attached to the reference sequence with only in one end (and other terminal of the sequence has not determined), so I cre…
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I am using canu 1.7 for assembling a genome of ~1.4gb size with ~70X pacbio data.
canu -p canu -d canu-pacbio useGrid=false maxThreads=60 maxMemory=500 genomeSize=1.4g -pacbio-raw file1 ....
I hav…
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I guess the input to the script would be:
1. the list of node IDs, created by the viewer application
2. some source of DNA for nodes in the assembly graph in question. for GFA/LastGraph files I gues…
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I generated a *.gfa file from an alignment in vg. When I run:
reveal bubbles -r ref test.hal2vg.gfa >test.hal2vg.bubbles
Traceback (most recent call last):
File "/usr/local/bin/reveal", line 1…
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Hi,
I'm having a similar issue like #546: https://github.com/marbl/canu/issues/546
The assembly step stops with the following error:
```-- Canu 1.6
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-- CITATIONS
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-- Koren S, Walenz BP, Be…