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Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2276 days ago Comments (1)
https://github.com/brentp/goleft
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license.
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Installing goleft
➜ falconUnzip_assembly bioconda install goleft
zsh: command not found: bioconda
➜ falconUnzip_assembly conda install goleft
Solving environment: done
## Package Plan ##
environment location: /home/urbe/anaconda3
added / updated specs:
- goleft
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2018.8.24 | ha4d7672_0 136 KB conda-forge
certifi-2018.8.24 | py36_1 139 KB conda-forge
goleft-0.1.18 | 1 6.6 MB bioconda
openssl-1.0.2p | h470a237_0 3.5 MB conda-forge
------------------------------------------------------------
Total: 10.4 MB
The following NEW packages will be INSTALLED:
goleft: 0.1.18-1 bioconda
The following packages will be UPDATED:
ca-certificates: 2018.8.13-ha4d7672_0 conda-forge --> 2018.8.24-ha4d7672_0 conda-forge
certifi: 2018.8.13-py36_0 conda-forge --> 2018.8.24-py36_1 conda-forge
openssl: 1.0.2o-h470a237_1 conda-forge --> 1.0.2p-h470a237_0 conda-forge
Proceed ([y]/n)? Y
Downloading and Extracting Packages
ca-certificates-2018 | 136 KB | ####################################################################################################################### | 100%
certifi-2018.8.24 | 139 KB | ####################################################################################################################### | 100%
goleft-0.1.18 | 6.6 MB | ####################################################################################################################### | 100%
openssl-1.0.2p | 3.5 MB | ####################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done