redundans

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Hi! I'm currently using Redundans, but when I was testing it I found that the Gapcloser step doesn't use the multithread option even when the option is provided. Any suggestion?...

aabaricalla

Hi, I am trying to follow your workflow in [Pryszcz et al., 2016](https://academic.oup.com/nar/article/44/12/e113/2457531?login=true#87015117) but I can't find in the repository the `fasta2diverged.py` script that you mention in the paper (neither...

MatteoSchiavinato

Hello, I am trying to run redundans software using paired ends, long reads and a draft assembly but I keep getting this error: [ERROR] Empty FastA file encountered: Do you...

mgarl-10

:eyes: Some source code analysis tools can help to find opportunities for improving software components. :thought_balloon: I propose to [increase the usage of combined operators](https://perldoc.perl.org/perlop#Assignment-Operators "Description for assignment operators") accordingly....

elfring

Hi I am use redundans with : "module load Python/2.7.16-GCCcore-8.3.0 /home/ulg/bbasv/daomhai/software/redundans/./redundans.py -v -i 350-R1.paired.fastq.gz 350-R2.paired.fastq.gz -f Catfish.asm.bp.p_ctg.fa -o Result" And it not work with the confirm ; " Options: Namespace(fasta='Catfish.asm.bp.p_ctg.fa',...

Hai1983

Was running redundans with contigs from a platanus-allee assembly, a reference genome of the same species, and some pacbio long reads. I am getting this error: [error log](https://github.com/JonEilers/error_logs/blob/main/redundans.log) command used...

JonEilers

new features

2

- AUTOMATISATION - [x] estimate read limit - [x] refine insert size estimation for each iteration - [x] include optional genome assembly step, is it really needed? - [x] include...

lpryszcz

scaffolding options

1

Hi there, I have a question about deciding between various read libraries for the scaffolding step in your pipeline. My input into your pipeline is a SPAdes hybrid assembly that...

bishopia

Install tmpfile

1

Addresses issue #66, so that INSTALL.sh can locate a log file.

waoki

mictadlo