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  • Jabba: Hybrid Error Correction for Long Sequencing Reads

Jabba: Hybrid Error Correction for Long Sequencing Reads

https://github.com/biointec/jabba

Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data.

Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE <node number> <size of node> <number of in edges> <in edges represented by node number of origin, separated by tabs> <number of out edges> <out edges represented by node number of target, separated by tabs>
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba-<input filename>.fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki