Commit 44e1d782 authored by peguerin's avatar peguerin
Browse files

README update

parent b6b522f1
......@@ -91,18 +91,30 @@ Platanus is a novel de novo sequence assembler that can reconstruct genomic sequ
```
platanus assemble -tmp temp/ -m 256 -t 64 -o serran_assemble -f pe_dir/*.fastq 2> assemble.log
platanus assemble -m 256 -t 64 -o serran_assemble \
-k 32 -s 10 -c 2 -a 10.0 -u 0.1 -d 0.5 \
-tmp temp/ -f pe_dir/*.fastq 2> assemble.log
```
### 2. Scaffoling
```
platanus scaffold -t 64 -tmp temp/ -c serran_assemble_contig.fa -b serran_assemble_contigBubble.fa -IP1 pe_dir/lib350bp_R*.fastq -IP2 pe_dir/lib550bp_R*.fastq -OP3 me_dir/lib3kbp_R*.fastq -OP4 lib5kbp_R*.fastq 2> scaffold.log
platanus scaffold -t 64 -tmp temp/ \
-c serran_assemble_contig.fa -b serran_assemble_contigBubble.fa \
-IP1 pe_dir/lib350bp_R*.fastq -IP2 pe_dir/lib550bp_R*.fastq \
-OP3 me_dir/lib3kbp_R*.fastq -OP4 lib5kbp_R*.fastq \
-s 32 -v 32 -l 3 -u 0.1 2> scaffold.log
```
### 3. Gapclose
```
platanus gap_close -t 64 -tmp temp/ -o serran_hpc_gapclose -c out_scaffold.fa -IP1 pe_dir/lib350bp_R*.fastq -IP2 pe_dir/lib550bp_R*.fastq -OP3 me_dir/lib3kbp_R*.fastq -OP4 lib5kbp_R*.fastq 2> gapclose.log
platanus gap_close -t 64 -tmp temp/ \
-o serran_hpc_gapclose \
-c out_scaffold.fa \
-IP1 pe_dir/lib350bp_R*.fastq -IP2 pe_dir/lib550bp_R*.fastq \
-OP3 me_dir/lib3kbp_R*.fastq -OP4 lib5kbp_R*.fastq \
-k 32 -s 32 -d 5000 \
-vo 32 -vd 32 -eo 1 -ed 0.05 -ro 0.66 -rs 0.9 2> gapclose.log
```
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment