SOAPdenovo

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

Workflow

1. Input clean paired-end reads
   Upload filtered paired-end FASTQ files, including clean R1 and clean R2 reads.

2. Build assembly configuration
   Generate a SOAPdenovo library configuration file using read length, insert size, and paired-end file paths.

3. Run de novo assembly
   Assemble reads with SOAPdenovo using the selected k-mer and assembly parameters.

4. Filter scaffolds
   Remove scaffolds shorter than 500 bp to keep reliable assembly sequences.

5. Generate scaftigs
   Break scaffolds at continuous N regions to produce N-free scaftig sequences.

6. Summarize assembly results
   Report scaffold number, total scaffold length, scaffold N50, scaftig number, and total scaftig length.

Data

Example dataset include 100 bp illumina WGS reads consist of ~10% subsets of 3 paired end sets of reads from the following publication:
The sample names in the original publication used to generate the toy dataset is ERR260162 (sample1)

Result

v0.3: The pipeline is stored in Code Repository: CRS1234220167039561728. The computational docker enrionment is stored in Software Repository: SRS1234224629351198720.

Reproducibility

The pipeline is stored in Code Repository: CRS1234220167039561728. The computational docker enrionment is stored in Software Repository: SRS1234224629351198720.

Usage

1. Select the application 'SOAPdenovo'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.