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Hi there,
It looks like the `-u` option has been removed since v2.1. Since I assume it is no longer supported, what is your advice for scaffolding Canu unitigs?
I was originally thinking I would…
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Hey when I try to run salsa:
python ~/SALSA-master/run_pipeline.py -a BW_racon3.pilon2_shasta.fasta -l BW_racon3.pilon2_shasta.fasta.fai -b BW_shasta.bed -e CATG -o scaffolds_shasta -m yes -g contigs…
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ABySS 2.2.5
Ubuntu 20.04.1 LTS
Genome Size: about 0.8Gbp
Coverage: about 60x
Data: Illumina 150bp paired-end, good quality runs
I have a couple of fish genome assemblies to do. All the fish h…
ms-gx updated
3 years ago
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Hi again. While rerunning my spacegraphcats run that had failed to finish in the allotted wall time, I ran into the follow warning/error during the bcalm_catlas_input rule. `Auks API request failed : …
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In the GFA output, all segments carry an optional field with the tag DA of type Z (printable string incl. whitespace). What is the meaning of this field?
At least in the output files I generated so f…
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Hi,
after the ecoli assembly is working I am trying a human assembly with a public datasets being split into the following runs:
ERR3518653, ERR3519640, ERR3522379, ERR3522985, ERR3528464, ERR3528…
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i tried to stitch unitigs.fasta file using
>python2 stitch.py -c xxx.contigs.fasta -u xxx.unitigs.fasta -p scaffolds_iteration_3.p -o output_scaffold_stitched_3p.fasta
I got error:
===============…
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Hi, I have got `miniasm: asm.c:267: ma_ug_seq: Assertion `sub[id].e - sub[id].s seq.l' failed.`
```
[M::main] ===> Step 0: removing contained reads Step 1: reading read mappings Step 2: 1-pass (…
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Hi, I'm new to Linux and Canu.
I have been reading issues #1336 #1108 #909, #901 as I am having the same problem.
My system is Ubuntu 18.
I installed canu using $conda install -c conda-forge -c bi…
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Would you be surprised if `abyss-sealer` does not change the BUSCO score at all? Why so or why not?
I am talking about `actinopterygii_odb10` db which contains 3640 total BUSCOs.
I get the follo…
ms-gx updated
3 years ago