Reference file format

[ardakdemir]

Hey ryan!

I am trying to incorporate rebaler to my assembly pipeline as the minimap2-miniasm-racon does not generate assemblies for the v0.5.1 version of Chirons basecalls.

Is there a specific format for the reference fasta files as input for Rebaler?

In addition, I find it hard to interpret the output of the rebaler. When I input rebaler with raw reads and a reference file it generates one assembly for each sequence in the reference file so I thought maybe there is something wrong that I am doing.

Below is the command I am using :

rebaler reference.fasta basecall.fastq > rebaler_assembly.fasta

If we have two sequences in reference.fasta it generates 2 sequences in the assembly.

Also for the references with the following headers I get assertion and key errors:

chr11 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

S00000410_C001 NODE_1_length_313850_cov_6.19914 TGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTA

This reference works fine 👍:

lambda length=48502 circular=true GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCG

Should i rename the reference file headers?

Thanks in advance.

Arda