spades

spades copied to clipboard

I know this might be a very minor issue but I did find out that, when running SPAdes by using the same name for the two fastq for the paired...

redsnic

FAQs, discussion group and/or issue template for common issues

2

I suggest to create FAQs, a discussion group and/or an issue template for frequently occuring common issues. It looks like that many issues created here at GitHub are related to...

tolot27

Stuck and segmentation fault

9

hi,@asl my command is 'metaspades.py -1 SRR9033753.rmhost.clean.1.fq.gz -2 SRR9033753.rmhost.clean.2.fq.gz -t 20 -o output' when I run it by SPAdes-3.14.1, the task stuck when Processing reverse paired-end reads. ` 0:00:39.478 2G...

liangzhengjiao

speeding up hmm-guided mode

2

Hi, I have been looking for ways to improve _de novo_ transcriptome assemblies from non-model species by using reference information from amino acid alignments (i.e. HMM profiles) of orthologous genes...

RAWWiberg

Stuck at subclustering hamming graph

4

I ran spades.py on my reads to have a plant genome assemby which has an estimated size of 600M. I am providng a memory of 998G but it was stuck...

amanpruthi15

Hello, I have some doubts about the assembly details of SPAdes.I know that ILLUMINA's paired-end reads must be provided when SPAdes performs metagenomic assembly (via "Using SPAdes De Novo Assembler")....

zhang-HZAU

3-15.1: .bin_reads/single_0.off: Unknown error 18446744073709551615

15

Hi, I have problems with rnaspades-3.15.1 (your 64-bit binaries) running on NFSv4 filesystem: ``` 0:00:00.094 1M / 11M INFO General (memory_limit.cpp : 48) Memory limit set to 2000 Gb 0:00:00.106...

mmokrejs

Assembly hangs at EC Threshold Finding stage

4

Hi, Sometimes a SPAdes assembly will hang indefinitely at `STAGE == EC Threshold Finding (id: ec_threshold_finder)`, at step `(kmer_coverage_model.cpp : 295) ... iteration 8`. However, if I add or remove...

chrisjackson-pellicle

How to deal with local modifications of llvm, specifically non-free ConvertUTF.*

2

Hi, in Debian we are trying to build the latest version of spades 3.15.1 but the locally modified copy of llvm creates problems we were not able to work around....

tillea

You can use Debian batches

4

Hi, I just learned that you can include badges into your web site / README.md to point users to the Debian packaged version of Spades. Just fill in `spades` into...

tillea