The Capture-Seq assembler

capture is an assembler developed to recover complete genome from ultra-high coverage samples

The repository is a work in progress and the assembler is not functional yet. Thanks for your interest and come back soon!

Installation

capture requires the following to be installed:

• python >= 3.6
• SPAdes

TODO

Quickstart

# paired-end reads, Illumina MiSeq
capture assemble -f reads_R1.fastq.gz -r reads_R2.fastq.gz \
--genome_size 35000 --mean 300 -o output_dir
# compressed paired-end reads, Illumina HiSeq
capture assemble -f reads_R1.fastq.gz -r reads_R2.fastq.gz \
--genome_size 35000 --mean 125 -o output_dir
# single end reads, Ion Torrent
capture assemble -u reads.fastq.gz \
--genome_size 35000 --mean 240 -o output_dir
# reads in bam format
capture assemble --bam reads.bam \
--genome_size 35000 --mean 240 -o output_dir
# full list of subcommands and options
capture -h
# full list of options for a subcommand
capture assemble -h

License

Code is under the MIT license

Contributing

We welcome contributions from the community! See our Contributing guide.