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We often get asked this. Users have compared to reference using Mauve and know how the contigs are ordered. They would like to be able to do this in PATRIC without having to do the manual, tedious p…
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## Input specifications
To skip the qc and assembly step we can provide the assemblies and reads used to generate the assemblies in a CSV file together with a CSV file specifying the reads.
The asse…
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I have identified a problem when running _shovill 1.1.0_ and passing the option `'--plasmid'` to _spades_.
### How to reproduce the problem
`shovill --outdir {output_folder} --R1 {R1_file} --R2 {R…
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Hi,
I wish to confirm that the LHE_COVERAGE parameter is the estimated coverage of long reads given to the assembler. Currently its description is difficult to interpret.
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Querying human reads to the human genome ([ref](ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz)) is very slow (~500 RPM, a **1000x…
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In https://github.com/ekg/freebayes/issues/419 @tseemann [asked if vg was ready for bacterial pangenomics](https://github.com/ekg/freebayes/issues/419#issuecomment-377646948). My response better fits …
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Dear @jenniferlu717 and @DerrickWood
Is there any way to resume a nearly-finished process for --download-library?
I was downloading the "bacteria" library (the biggest one, nearly 140 GB) and I g…
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Hello,
I am trying to use megahit as part of a larger analysis pipeline, and have encountered a strange behavior. I produced a test set using the following steps:
1. Extracted a 1M genomic sequence …
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This is a collection of ideas that should be considered after the DSL2 conversion #56 is finished. The list is subject to change. Any ideas or discussions are welcome.
#### Preprocessing (check out…
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Hi,
I am getting the below segmentation fault from buildPosMap. I am running MaSuRCA 3.2.6.
The assembler continues despite this issue and appears to complete correctly so I assume it is not a cri…