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[23] clipcrop
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# INPUT INFORMATION
# SAM FILE : 8.sam
# FASTA FILE : /usr/local/bin/ref/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa
# JSON FILE : null
# OUT…
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Hi
In the Cactus paper (https://www.biorxiv.org/content/10.1101/730531v3) it mentions that it expects the input genomes to be soft-masked. I was wondering how Cactus treats the soft-masked regions.…
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whole genome association analysis toolset
https://www.cog-genomics.org/plink2
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Hello,
I'm currently analyzing a substantial dataset comprising 11,743 genomes of different _Enterococcus_ species, including over 20 outgroup genomes from the same family and order. because of the…
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Hi,
When trying to run the following command with version 2.0.1
```
$BNG_DIR/runBNG denovo \
-t /BiO/Access/cdmm92/resource/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/11442…
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I have a workflow which uses kmc to count all kmers in an extremely large dataset of about 250,000 fasta files. The workflow was originally built with v3.2.1 of kmc, but stalled when I updates to v3.2…
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(Moved here from https://github.com/broadinstitute/pooled-cell-painting-analysis/issues/83)
Right now, the workflow has several stages and/or proposed stages
1. CellPainting illumination correc…
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There are a number of fields in the GROW dataset that need to be mapped to fields in the NMDC schema, so that the data can be effectively translated and a JSON can be produced.
| GROW …
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Hi Bakta developers!
Thank you for a great tool for plasmid and bacterial genome annotation!
I am using Bakta specifically to annotate the origin of replication. In some of my plasmid genomes, Ba…
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HI,
I am interested in checking a bat assembly using craq. I installed it using conda. Installation went fine, supposedly, but then it failed when I tried to run it using short-read data that I mappe…