Chirag Jain

boolean spgemm: can I avoid numeric phase?

4

I'm using spgemm for an application in biological data analysis. In my application, I've boolean matrices, and I'm only interested in boolean matrix multiplication. From the output, I only need...

Question regarding -L (min variant length) parameter

3

Ideally, `-L 1` should include maximum number of variants in genome graph, but this does not happen. Please see the runs below: ``` $ minigraph -cxggs -L 2 hap1.chr18.fa hap2.chr18.fa...

Many thanks for providing this library! I'm using the following code snippet as part of my application ``` csa_wt fm_index; construct_im(fm_index, "mississippi!", 1); std::cout

Segmentation fault

1

Hello, I wish to test astarix on small test data available in [minigraph repository](https://github.com/lh3/minigraph/tree/master/test). The graph is in GFA format with zero overlaps. For this, I ran the following command:...

Support for simulating more recent base-callers Guppy 3.6

2

Hi, Thanks for providing this tool. As ONT raw accuracy is rapidly improving, I wanted to check if you're able to support base-calling using ONT's latest protocols. Currently, ONT provides...

Comparing minigraph and Dipcall

1

Dear Heng, I and @gsc74 tried to compare minigraph and Dipcall SV calls by using HG002 HiFi diploid assembly. We used a similar method for comparison as how you had...

Question about Hifiasm algorithm

2

In the review article "Genome assembly in the telomere-to-telomere era", @lh3 and @richarddurbin have mentioned that: > When constructing an overlap graph, we discard a read contained in longer reads....

Interpretation of bed files

1

``` $ cat prefix.dip.bed | awk 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}' 2823519412 $ cat prefix.hap1.bed | awk 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}' 2690214366 $ cat prefix.hap2.bed | awk 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}'...

There is already an option`greater-than N` for printing kmers that occur more than N times in the input. It would also be nice to have a similar option `most-frequent x`...

Can user provide seed to random generator during read simulation?

2

It seems like the seed value is fixed for read simulation: https://github.com/marbl/seqrequester/blob/31141c14d80fe0dde2766bcc3e622bf600e2bba4/src/seqrequester/simulate.H#L59 Is it possible to expose this parameter on the command line interface?