recipe secapr

Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing, producing haplotype alignments.

Homepage

https://github.com/AntonelliLab/seqcap_processor

License

MIT

Recipe

/secapr/meta.yaml

package secapr

(downloads) docker_secapr

Versions

1.1.15-1, 1.1.15-0, 1.1.14-0, 1.1.12-0, 1.1.10-2, 1.1.10-0, 1.1.9-0, 1.1.8-0, 1.1.7-0, 1.1.4-0, 1.1.0-0, 1.0.2-0, 1.0.1-0

Depends abyss

Depends bcftools

1.8

Depends biopython

Depends bwa

>=0.7

Depends cogent

Depends emboss

Depends fastqc

Depends lastz

Depends mafft

>=7.2

Depends muscle

Depends numpy

Depends pandas

Depends picard

Depends python

>=2.7,<2.8.0a0

Depends samtools

0.1.19.*

Depends seqtk

>=1.0.82,<=1.2

Depends trimmomatic

0.33

Depends trinity

<=2.3.2

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install secapr

and update with:

conda update secapr

or use the docker container:

docker pull quay.io/biocontainers/secapr:<tag>

(see secapr/tags for valid values for <tag>)