Hello,
I have been running the NOVOPlasty for a while but still don´t get how it works, I have my raw data from MiSeq Illumina PE reads. After trimming the indexes I want to do the assembly with the NOVOPlasty, which asks for a "Seed". I have tried many and different seeds, but I get always the same result. The NOVOPlasty assembly selects a thousand of reads ONLY covering the SEED length, then it stops. I also don´t get why the NOVOPlasty asks you to not trim the reads, and if this has something to do with my problem
This is my script line:
perl /trinity/shared/easybuild/software/NOVOPlasty/3.7-GCCcore-8.3.0/NOVOPlasty3.7.pl -c /path_to_/config.txt
config.txt is:
Project:
Project name = Test Type = chloro Genome Range = 120000-200000 K-mer = 20 Extended log = 0 Save assembled reads = no Seed Input = /path/Seed.fasta (#Seed is about 600 bp, also tried with ca 1000 bp) Extend seed directly = no Reference sequence = /path/reference.fasta (#also tried without ref file) Variance detection = yes Dataset 1:
Read Length = 151 Insert size = 300 Platform = illumina Single/Paired = PE Combined reads = Forward reads = /path/R1_paired.fastq Reverse reads = /path/R2_paired.fastq
Insert size auto = yes Use Quality Scores = yes I would appreciate your help, thanks, Belen
