The Capture seq assembler
Project description
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Close
Hashes for capture_assembler-0.1.0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 6da6051abd51b51d0b633896b80a6547c1d469e73f29e2698b807e5d8f8a2955 |
|
MD5 | 161b9b0c9c050fc63f8e5a4db0a134c7 |
|
BLAKE2b-256 | 6452713f80e1928e92d92149ad56a2c5cd40496ab6053e078de6e495336e4137 |