Error models¶
Pre-built models¶
Qualities¶
The prebuilt models were built with the following commands:
megahit -1 reads_R1.fastq -2 reads_R2.fastq -o asm
bowtie2-build asm/final.contigs.fa miseq_asm/final.contigs
bowtie2 -x asm/final.contigs -1 reads_R1.fastq \
-2 reads_R2.fastq | samtools view -bS | samtools sort -o mapping.bam
samtools index mapping.bam
iss model -b mapping.bam -o name_of_model
The MiSeq model was built from an ocean metagenomics project in Kenya (sample accession number ERR1912174).
The HiSeq and NovaSeq models were built from human run obtained via basespace.
Creating an Error Model¶
If you do not wish to use the pre-computed error models provided with InSilicoSeq, it is possible to create your own.
InSilicoSeq creates error models from .bam files. The input bam file should be a set of reads aligned against a reference genome or metagenome.
Given you have two read files, reads_R1.fastq.gz and`reads_R2.fastq.gz`, and a reference metagenome ref.fasta:
Align you reads against the reference¶
bowtie2-build ref.fasta ref
bowtie2 -x ref -1 reads_R1.fastq.gz \
-2 reads_R2.fastq.gz | samtools view -bS | samtools sort -o ref.bam
samtools index ref.bam
Build the model¶
iss model -b ref.bam -o my_model
which will create a my_model.npz file containing your newly built model
Full list of options¶
–bam¶
aligned reads from which the model will be inferred (Required)
–model¶
Error model to build. If not specified, using kernel density estimation (default: kde). Can be ‘kde’ or ‘cdf’
–output¶
Output file prefix (Required)
–quiet¶
Disable info logging
–debug¶
Enable debug logging