ggcat

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GGCAT keeps panicking about too many open files

1

I'm trying to run GGCAT on the following dataset: https://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/ I had 5T of free disk space and the following flags: `-k 31 -m 32 -j 8 -s 1` However,...

iosfwd

Plans to generate a GFA?

1

Hi, Do you have any plans to produce a GFA output instead of a Fasta? it would be a natural way to represent the full graph with adjacency information betw...

rlorigro

access datasets of origin

2

Hi, I would need an option to access the original datasets of each unitig constructed by GGCAT. The output could be heavy, but a first idea would be to write...

kamimrcht

Change number of dedicated threads

2

Hi @Guilucand — When processing some data with GGCAT, @jamshed and I noticed that sometimes the number of threads in use can _substantially_ exceed the thread count requested by the...

rob-p

Problem with GGCAT when using 32 threads

1

I was running ggcat on 72 human genomes (subset of human genomes used in ggcat paper and published on zenodo). I was executing it with 32 threads. After 24 hours...

khodor14

Hi! Can you provide binaries for Linux here or on bioconda to simplify the installation process? Thanks

enricorox

Coloring options for an input file list

4

Hi, Would it be possible to add an option to supply a list of colors to use when building a colored DBG from an input file list? The current method...

tmaklin

different runs return different number of unitigs and distinct color subsets

6

Hello @Guilucand and @alexandrutomescu. Let me first congratulate with you for this excellent algorithm! We are currently using GGCAT for building [Fulgor](https://github.com/jermp/fulgor), a colored k-mer index based on SSHash (same...

jermp

Hi, I am wondering if I can get the kmer counts along with the unitigs fasta files. Thanks, Moustafa

shokrof