Source code for the SOAPdenovo2 genome assembling pipelines
This is an introduction for reproducing the assembly results mentioned in the manuscript of SOAPdenovo2.
YH genome assemblies
- Decompress the file YH_pipeline.tgz: tar xvfz YH_pipeline.tgz.
- There are four command shells, representing four assemblies:
- run_1.0.sh: Use SOAPdenovo1 pipeline to assemble the YH genome.
- run_2.0.sh: Use SOAPdenovo2 standard pipeline to assemble the YH genome, you can enable multi-k-mer mode in this pipeline.
- run_sparse.sh: Enable SOAPdenovo2 sparse DBG mode to assemble YH genome.
- run_sparse_muti_test.sh: Enable both the SOAPdenovo2 sparse DBG mode and multi-k-mer mode to assemble the YH genome.
- For each assembly, there are 9 steps including data download, read filter, error correction, assembly and gap closure. So you need to check whether each step has finished correctly.
- To get the final assembly results, if you only proceeded to the scaffolding (.scaff.) step in SOAPdenovo, you can find the genome sequence with a file name: "assembly/.scafSeq". If you have finished all the steps including GapCloser, you can find the final genome sequences file named as "gapcloser/.scafSeq.GC".
To assembly GAGE data:
There are three datasets of GAGE assembled by SOAPdenovo, so we have three pipelines that should be decompressed respectively:
Before running the assembly, you need to download the reads and put them into the correct locations:
- Download the three compressed datasets from http://gage.cbcb.umd.edu/data/.
- Decompress the datasets and put the reads into the corresponding Data folder.
Each genome has two command shells:
- SOAPdenovo1_pipeline.sh: Use SOAPdenovo1 pipeline to assemble the data in working directory.
- SOAPdenovo2_pipeline.sh: Use SOAPdenovo2 pipeline to assemble the data in working directory.
The final assembly sequence file is named as "*.scafSeq.GC.fa";
To assembly Assemblathon1 data:
Decompress the file: Assemblathon1_pipeline.tgz.
The Assemblathon1 assembly including two datasets:
- Bacteria (contamination) sequence database: you can download it from ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz
- Assembly data: the pipeline will download the data automatically, if you have these data already, please read the README carefully in the Assemblathon1_pipeline.
After all the datasets are ready, please run the command shell: run.sh: Use SOAPdenovo1 and SOAPdenovo2 pipeline in serial to assemble the Assemblathon1 reads.
The final assembly sequence file is named as "consensus/*.scafSeq.GC.filter";
For more details, please refer to the README in each pipeline.