Dear users, we have installed a new software: HapCUT2 v1.3.3:
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HapCUT2: HapCUT2/v1.3.3
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Description:
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype
assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others. With this in mind, HapCUT2 is designed for speed and accuracy across
diverse sequencing technologies, including but not limited to: - NGS short reads (Illumina HiSeq) - single-molecule long reads (PacBio and Oxford Nanopore) - Linked-Reads (e.g. 10X Genomics, stLFR or
TELL-seq) - proximity-ligation (Hi-C) reads - high-coverage sequencing (>40x coverage-per-SNP) using above technologies - combinations of the above technologies (e.g. scaffold long reads with Hi-C
reads)
You will need to load all module(s) on any one of the lines below before the "HapCUT2/v1.3.3" module is available to load.
GCC/12.3.0
Help:
Description
===========
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads,
designed to "just work" with excellent speed and accuracy.
We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols,
with slow or inaccurate performance on others.
With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies, including but not limited to:
- NGS short reads (Illumina HiSeq)
- single-molecule long reads (PacBio and Oxford Nanopore)
- Linked-Reads (e.g. 10X Genomics, stLFR or TELL-seq)
- proximity-ligation (Hi-C) reads
- high-coverage sequencing (>40x coverage-per-SNP) using above technologies
- combinations of the above technologies (e.g. scaffold long reads with Hi-C reads)
More information
================
- Homepage: https://github.com/vibansal/HapCUT2/
Best,
HPC team