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Hi Glenn!
I'm currently running `cactus-hal2maf` on a new alignment I've generated using Cactus v2.8.2. I'm running Cactus as a singularity image on a computing cluster. Anyways, I have an alignmen…
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-searching for reference exome (CDS) as a reference for our exome sequence data due to several reasons:
1- when we aligned to one chromosome like chr 20, the alignment rate was v.v low 2.8%
2- whe…
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Dear,
We've been using roary with pleasure the last few months, so thanks for this awesome piece of software!
However, we're missing out on one certain feature: adding an outgroup to the core gene a…
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TODO: Fix the 28-bit limit on CIGAR length size in the internal memory structures.
While we have no immediate plans to support reads several Gb long, we do support references this long now.
Howe…
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Thanks for the good material. I have a question about the alignment using bowtie2, here according to [`mutation_sequencing_analysis_script.sh`](https://github.com/aldob/iMUT-seq/blob/4476db76f2058d0af…
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[Breaking Lander-Waterman's Coverage Bound](http://biorxiv.org/content/early/2016/06/23/060384) - assembly
[Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads.](https://w…
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Hi vg team,
I recently ran `vg stats -a` on my sample GAM file (`sample.gam`) generated from a whole-genome sequencing project and observed a low count of "Total perfect" reads. I'm seeking some in…
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The webpages (https://sanger-pathogens.github.io/Roary/) said We cannot use the output of Roary as the input to Gubbins, do you mean the "core_gene_alignment.aln" file cannot be used as the input to G…
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Hi,
I get this kind of error every couple of screens during RunLastzChain.sh (http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto#Example.2C_step_1:_Alignments_with_Blastz) execution an…
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Hello,
Wanted to share the following error obtained when running MTase-linker.
```
Traceback (most recent call last):
File "/localdata/researchdrive/gkanaan/tools/ML_dependencies/ML_envs/06b…