b-ummi / lmas Goto Github PK

Update script to include the latest version of the samples

• ENN - even without error
• EMS - even with miseq error
• LNN - log without error
• LHS - log with hiseq error
• about.md

Add the following params:

/*
Assembly Quality Control
*/
minLength = 1000
mapped_reads_threshold = 0.75
/*
Quality Parameters
*/
n_target = 0.5
l_target = 0.9

Mention that specific assembler related params are available at params.config file

Hi,

It's a perfect soft!

How to use this soft? when I run the following command, but it does not work, would you mind giving me some suggestions?

(lams) deyuan@deyuan:/media/deyuan/NCBI/Norgal_animal_data$ LMAS --fastq SRR2089775 --megahit --megahitKmerSize --reference /media/deyuan/NCBI/Norgal_animal_data/SRR2089775/2.NOVOPlasty/Circularized_assembly_1_SRR2089775.fasta
N E X T F L O W ~ version 23.04.1
Launching /home/deyuan/miniconda3/envs/lams/share/lmas-2.0.x/main.nf [soggy_lichterman] DSL2 - revision: 929afaa022
Trace file already exists: /media/deyuan/NCBI/Norgal_animal_data/pipeline_stats.txt -- enable the 'trace.overwrite' option in your config file to overwrite existing files
(lams) deyuan@deyuan:/media/deyuan/NCBI/Norgal_animal_data$

deyuan

Per assembler, the contigs IDs are being merged on all traces of the position of the alignment blocks.