BOL: HALC: High throughput algorithm for long read error correction

HALC: High throughput algorithm for long read error correction

Jit — Fri, 08 Jun 2018 10:47:41 -0500

HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach) HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.

Address of the bookmark: https://github.com/lanl001/halc

Comment by Jit

Jit — Mon, 13 Aug 2018 18:12:06 -0500

Inputs
- Long reads in FASTA format.
- Contigs assembled from the corresponding short reads in FASTA format.
- The initial short reads in FASTA format (only for -ordinary mode; obtained with cat left_reads.fa >short_reads.fa and then cat right_reads.fa >>short_reads.fa).

Using AlignGraph

runHALC.py long_reads.fa contigs.fa [-options|-options]