Skip to main content

The Capture seq assembler

Project description

The Capture-Seq assembler

Build Status made-with-python LICENSE

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!


capture requires the following to be installed:

  • python >= 3.6
  • SPAdes



# 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


Code is under the MIT license


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

Project details

Release history Release notifications

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
capture_assembler-0.1.0-py3-none-any.whl (13.7 kB) Copy SHA256 hash SHA256 Wheel py3 Jun 28, 2018
capture-assembler-0.1.0.tar.gz (1.6 MB) Copy SHA256 hash SHA256 Source None Jun 28, 2018

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page