REPdenovo
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simoncchu
A tool to construct repeats directly from raw reads
It seems REPdenovo requires Python2 and does not run on python3. However python2 is end-of-life (https://pythonclock.org/ ). Are there any plans to have REPdenovo run on python 3 ?
Hi! This issue appears to have some similarities to another open issue (#11) entitled [TERefiner_1 error](https://github.com/simoncchu/REPdenovo/issues/11). I ran REPdenovo and produced a `contigs.fa` file. I found no obvious errors or...
Hi, when running REPdenovo, the program stops with the following error: Running command: ./TERefiner_1 -P -b ./test/contigs.fa.itself.sort.bam -r ./test/contigs.fa -o ./test/contigs.fa_no_dup.fa -c 0.9 -g ... /bin/sh: ./TERefiner_1: cannot execute binary...
This is a report of issues with the variable ending in "_PATH" on the configuration file (with a fix). The configuration file for REPdenovo's main.py take several paths to different...
Hi Chong, I'am from France and I think I have some problems with TERefiner_1. I wanted to know is it important for the rest of my analyzes? I obtain my...
cd TERefiner && make && cd .. = after this command fatal error api/BamReader.h: No such file or directory compilation terminated is generating. g++ -O3 -Wall -static -I../bamtools/build/src/api/include -I../bamtools/build/src/include -L...
Hi @Reedwarbler i'm testing REPdenovo but i do not undersand my ouputs here the output error : [output_error.txt](https://github.com/Reedwarbler/REPdenovo/files/1974158/output_error.txt) my configuration file: [config_file.txt](https://github.com/Reedwarbler/REPdenovo/files/1974162/config_file.txt) the read_file: [read_file.txt](https://github.com/Reedwarbler/REPdenovo/files/1974166/read_file.txt) and the three output_files wich...
Hi, I'm student in intership in a Lab in France. So i rread many times your review while my bibliography project. So now i'm testing your tool and i get...
