Metagenome Assembly
Input
Up / Downstream Reads: Choose the files containing the paired-end reads respectively. SPAdes is not able to continue if the number of upstream reads doesn't exactly match the number of downstream reads, or if the read names differ.
Read Orientation: For forward-reverse orientation, the forward reads correspond to the left reads, and the reverse reads, to the right. Similarly, in reverse-forward orientation left and right reads correspond to reverse and forward reads, respectively.
Figure 1. MetaSPAdes assembly wizard: input page.
Configuration
K-mer sizes: SPAdes will automatically select the k-mer sizes for graph construction. If desired otherwise, please provide a comma-separated list of odd k-mer sizes (1-128).
Figure 2. MetaSPAdes assembly wizard: configuration page.
Output
Contigs Fasta: Choose where to save the resulting multi-fasta file.
Scaffolds Fasta: Choose where to save the resulting file containing the scaffolds.
Figure 3. MetaSPAdes assembly wizard: output page.
Input
Sequencing Data: Choose the type of input data: single-end, paired-end or interleaved paired-end reads If paired-end is selected, two files per sample are required and the file pattern has to be provided.
Input Reads: Provide the files containing sequencing reads. These files are assumed to be in FASTQ / GZ format.
Paired-end configuration: When working with paired-end libraries, a so-called pattern has to be established to help the software distinguish between upstream and downstream read files. Per default, we assume the following pattern:
upstream: SampleA_1.fastq
downstream: SampleA_2.fastq
Note:
For example, if the upstream file is named SRR037717_1.fastq and the downstream one SRR037717_2.fastq, you should establish "_1" as the upstream pattern and "_2" as the downstream pattern.
Figure 4. MEGAHIT assembly wizard: input page.
Configuration
Minimum Multiplicity: K-mers that appear less times are filtered out. (kmin+1)-mer with multiplicity lower than d will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly.
K-mer Sizes: Provide a list of k-mer sizes for iterative graph creation. Values have to be odd and in the range 15-255.
for ultra-complex metagenomics data such as soil, a larger kmin, say 27, is recommended to reduce the complexity of the de Bruijn graph. Quality trimming is also recommended.
for high-depth generic data, large
--k-min(25 to 31) is recommended.smaller
--k-step, say 10, is more friendly to low-coverage datasets.
No Mercy K-mers: Do not add mercy k-mers. Mercy k-mers are specially designed for metagenomics assembly to recover low coverage sequences. For generic dataset >= 30x, MEGAHIT may generate better results with
--no-mercyoption.Bubble Level: Intensity of bubble merging. Bubbles occur in the de Bruijn graph when several paths start in the same vertex and end in another vertex together.
Bubble Merge Level L: in complex bubbles with length <= L * k-mer size are merged.
Bubble Merge Level S: Complex bubbles with similarity >= S are merged.
Prune Level: Strength of low depth pruning.
Prune Depth: Remove unitigs with average k-mer depths less than this value.
Low Local Ratio: Ratio threshold to define low local coverage contigs.
Max Tip Length: Remove tips shorter than this value.
Disable Local Assembly: The local assembly module was introduced in version 1.0 and creates local contigs between iterations with high confidence k-mers.
Figure 5. MEGAHIT assembly wizard: configuration page.
Output
Contig Fasta: The final fasta file containing the assembled contigs, will be saved in this file location.
Figure 6. MEGAHIT assembly wizard: output page.