Alexis Groppi

Hi, Thanks for your answer `LAsplit -v Stella.# 10 < Stella.las` worked well But the next step (HINGE filter) give a segmentation fault : ``` /home/ag/HINGE/inst/bin/hinge filter --db Stella --las...

Same bug again : the ouput and error file is about 2Go ! and still growing WITH empty lines or spaces !! Here is the content of the output folder...

Thanks Does that mean that in the next steps : `hinge maximal --db Stella --las Stella.las -x Stella --config /home/ag/HINGE/utils/nominal.ini` `hinge layout --db Stella --las Stella.las -x Stella --config /home/ag/HINGE/utils/nominal.ini...

Hi, Actually it does affects the rest of the pipeline. Next step : ``` hinge draft-path $SLURM_SUBMIT_DIR Stella Stellahinge_3kb.G2.graphml hinge draft --db Stella --las Stella --prefix Stella --config /home/ag/HINGE/utils/nominal.ini --out...

Thanks for your advice. I'll try and will tell you how it goes

@gtamazian using chromosomer fragmentmap's ratio threshold 1.05 greatly improved the final assembly : All chromosomes are present and the size is ~178 Mb The reference genome (close species) contains 8...

Actually, after many tries, changing the parameters of blastn (from default to `-perc_identity 40 -word_size 28 -evalue 50`) doesn't change anything. The only parameterwho influence the final assembly is the...

Thank you for you for your answer and this advice. Strange for me because I'm using very closely related genomes (peach vs apricot) I will try Satsuma. Thanks again

I have masked both (reference and my dreft assembly with repeatmasker 4.0.7 : `RepeatMasker -species arabidopsis -pa 20` How do you check the alignments (if they are split in short...

Hi YES there is a file called `000191F_reads.fa` under the directory `3-unzip/reads/`