110allan/ccsx

efficient tool for generating circular consensus sequences (ccs) from subreads.

ccsx

efficient tool for generating circular consensus sequences (ccs) from subreads.
Ccsx works with both x86-64 CPUs and ARM CPUs supporting the NEON instruction sets(https://github.com/DLTcollab/sse2neon.git).
Efficiency is guaranteed with the use of bsalign(https://github.com/ruanjue/bsalign.git)

install

X86_64:
git clone https://github.com/110allan/ccsx.git
cd ccsx
git clone https://github.com/ruanjue/bsalign.git
make
./ccsx -h

ARM64:
git clone https://github.com/110allan/ccsx.git
cd ccsx
git clone https://github.com/DLTcollab/sse2neon.git
git clone https://github.com/ruanjue/bsalign.git
make
./ccsx -h

usage

Usage : ccsx [options]
Generate circular consensus sequences (ccs) from subreads.

Options:
-h Output this help
-v debug
-m Minimum total length of subreads in a hole to use for generating CCS. [5000]
-M Maximum total length of subreads in a hole to use for generating CCS. [500000]
-c Minimum number of subreads required to generate CCS. [3]
-A For fasta/fastq input,gzip allowed
-P primitive bsalign,subread shred by default
-X Exclude ZMWs from output file,a comma-separated list of ID
-j Number of threads to use. [2]

Arguments:
input Input file.
output Output file.

ccsx's Issues

Which license is this project released under?

As the maintainer of SSE2NEON, I am excited about the DNA research adoption. However, it is not clear to me for the licensing terms when I checked the source code. Can you clarify?