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Eagle Genomics (@EagleGenomics-cookbooks)

EagleGenomics-cookbooks

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elPrep

Cookbook to install elPrep: a high-performance tool for preparing sequence alignment/map files in sequencing pipelines.

R

Cookbook for installing R

QIIME

Cookbook for installing QIIME

cutadapt

cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

TrimGalore

This cookbook installs TrimGalore: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.

reapr

Cookbook to install REAPR: a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison.