GEAR hosts the halo web application at https://www.gear-genomics.com/halo/. The halo command-line tool is needed to compute the input file for the halo web application.
The halo command-line tool is available as a pre-compiled statically linked binary from Halo's github release page, as a singularity container SIF file or as a minimal Docker container.
git clone --recursive https://github.com/gear-genomics/halo.git
cd halo/
make all
make installHalo is used to create the input JSON file for the web application.
./bin/halo -hThis command-line application was designed for Strand-Seq single-cell DNA data but the viewer can also be used for any haplotype-resolved data. To convert the Strand-Seq alignment data into JSON format please provide one input BAM file for each input cell, e.g.:
halo count -g hg38.fa -o sc.json.gz sc1.bam sc2.bam sc3.bamThe output file sc.json.gz can then be uploaded and visualized at https://www.gear-genomics.com/halo/.
Besides Strand-Seq data, halo can also be used on any haplotype-tagged BAM file that uses the HP tag.
halo count -r -t HP_tagged -w 25000 -g hg38.fa input.bamThis command generates coverage data by haplotype using 25Kbp windows. The output file can then be uploaded and visualized at https://www.gear-genomics.com/halo/.
Halo is distributed under the GPLv3 license. Consult the accompanying LICENSE file for more details.
HTSlib is heavily used for all genomic alignment variant processing. Boost for various data structures and algorithms.