cuttlefish

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update to KMC fork to eliminate patching and allow compilation on AMD w/SIMD

3

refresh-bio KMC (https://github.com/refresh-bio/KMC) is a dependency, but has some compilation issues that prevent available instruction set detection on AMD. I have changed the CMake dependency to a fork of KMC...

ggraham

arm64 Cuttlefish on bioconda

4

Hello! I see that v2.2.0 adds support for compiling on M1/M2 architectures; however, I don't think these have been [added to bioconda](https://anaconda.org/bioconda/cuttlefish) yet. Are there plans to upload them as...

aryakaul

Reduced GFA output --> GFA1/GFA2 Output

1

Hello! Thanks for Cuttlefish, it's been working nicely for me so far. I've been using the reduced GFA format for my own analysis, but have occasionally come across tools that...

aryakaul

is there a way to get the kmer counts of the kmers in the produced unitigs?

4

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

shokrof

Would you mind providing a more detail on assembly ?

2

Hi, It's a perfect soft. When I used it to assemble my data, I could not understand the --read parameter, if I have data like R1_fq.gz, and R2_fq.gz， how to...

deyuanyang

Patch step error while linking library with CMake

3

Hi, I'm attempting to link your library with a combination of `FetchContent` and `add_custom_target`. Everything installs great, but when I link KMC (the one built by your CMakeLists) in order...

rlorigro

Potential arm support?

3

Hi! Would you be interested in arm support in future? I gave it a shot today and and think the `-m64` CFLAG in the kmc patch precludes this. Thanks!

michaelbarton

Extra large kmer

6

Dear cuttlefish authors, Thank you for this useful tool. I have a large database of genomes and I want to reduce the redundancy to reduce the computational time, improve speed...

apaytuvi

tools for the result of cuttlefish?

1

I want to use cuttlefish to my WGS popupation including 500 accessions. When get ucontigs for all accessions, I am not very clear to how to do next step analysis,...

shenweima

question on graph compaction

1

Hi thank you for cuttlefish, I have an output from cuttlefish at k=31 The unitigs don't seem to be maximal, there are multiple unitigs in a row shouldn't they be...

kevyin