Assembly using miniasm+racon

A recent preprint described a fast approach for assembling and correcting PacBio and MinION data. The principle is:

  • using minimap for fast all-against-all overlap of raw reads
  • using miniasm, this “simply concatenates pieces of read sequences to generate the final sequences. Thus the per-base error rate is similar to the raw input reads.”
  • mapping the raw reads back to the assembly using minimap again
  • using racon (‘rapid consensus’) for consensus calling
  • perform the racon step at least twice

Running miniasm and racon on MinION data

All-against-all overlap with minimap

Note how the reads are used twice here, as we map the reads against themselves:

minimap -Sw5 -L100 -m0 \
-t 2 \
/data/assembly/MAP006-1_2D_pass.fastq \
/data/assembly/MAP006-1_2D_pass.fastq \
| gzip -1 >racon_MAP006-1_2D_1.paf.gz

The output is in the so-called PAF (Pairwise mApping) Format, and is compressed ‘on the fly’.

Assembly with miniasm

miniasm takes the paf file and produces an assembly in GFA (Graphical Fragment Assembly) format.

miniasm -f /data/assembly/MAP006-1_2D_pass.fastq \
racon_MAP006-1_2D_1.paf.gz \

Since we have only one sequence in the GFA file (at least for this assembly), we can use a simple set of unix commands to turn it into a fasta file:

head -n 1 racon_MAP006-1_2D_1.gfa | awk '{print ">"$2; print $3}' > racon_MAP006-1_2D_1.raw_assembly.fasta

Correction with racon, round 1

We first use minimap again, this time with the original reads mapped against the ‘raw’ assembly:

minimap racon_MAP006-1_2D_1.raw_assembly.fasta \
/data/assembly/MAP006-1_2D_pass.fastq \

racon is basically run as racon -t num_threads reads.fastq mapped_reads.paf assembly.fasta consensus.fasta:

racon -t 2 \
/data/assembly/MAP006-1_2D_pass.fastq \
racon_MAP006-1_2D_1.raw_assembly.reads_mapped.paf \
racon_MAP006-1_2D_1.raw_assembly.fasta \

This will take some time.

Correction with racon, round 2

Run the mapping with minimap and the correction with racon again, but now with the results of the first round of correction as input. Please be careful when naming files!

Running miniasm and racon on PacBio data

Use all available reads from the P6C4 run, i.e. :


The commands are the same as for the MinION data. Again, please be careful when naming files!