{"repo":"sneuensc/mapache","free":true,"listed":false,"github":"https://github.com/sneuensc/mapache","clone":"git clone https://github.com/sneuensc/mapache.git","description":"mapping pipeline for ancient DNA","language":"Python","stars":35,"topics":["adna","ancient-dna","genomics","mapping","mapper","pipeline","workflow","snakemake","fastq","bam"],"license":"GPL-3.0","category":"workflow-automation","readme_excerpt":"Mapache Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit the Wiki for extensive documentation on how to use mapache and follow the tutorial to map and impute the test dataset. If you already have some experience with DNA mapping and/or Snakemake, you can follow the quick guide below. The usage of this workflow is described in the Snakemake Workflow Catalog. The following main steps are included in mapache : Moreover, mapache allows you to map large datasets to a single reference genome or to multiple genomes. Mapache is designed having in mind that one or multiple DNA libraries are generated per sample, and such libraries are sequenced at least once (e.g., for screening), but usually multiple times (normally prioritizing the highest-quality libraries). This results in several FASTQ files, which have to be mapped several times over the course of a project in order to generate a single BAM file. The goal of mapache is to make the mapping process as easy and transparent as possible, whether you are mapping to a single or multiple genomes, mapping for the first time, needing to update a BAM file or even impute low-coverage genomes. Quick guide To install mapache, you need to clone the repository and create a conda environment following the instructions below. This will automatically install the software needed to map FASTQ files to a reference genome and create a report with the mapping statistics. To execute ma","default_branch":null,"files":null,"tree":[],"storefront":"/r/sneuensc","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/sneuensc/mapache/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}