MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization

Abstract

Supplementary data are available at Bioinformatics online.

A Genome-Wide Screen Identifies Genes in Rhizosphere-Associated Pseudomonas Required to Evade Plant Defenses

“…Bottlenecks have previously been observed for other host-associated Tn-Seq screens ( 14 ). We adjusted our analysis to account for bottlenecks by first combining all reads per gene and then averaging the 3 replicates per gene ( 18 ).…”

“…Data analysis was performed using Galaxy and a modified version of the MaGenTA pipeline described previously ( 18 ). Our custom adapters and barcodes are shown in Data Set S1 , and a schematic of library construction is shown in Fig.…”

Genome-wide discovery of novel M1T1 group A streptococcal determinants important for fitness and virulence during soft-tissue infection

“…We monitored the composition of the GAS 5448 Krmit pool en masse to determine differential mutant abundance using DEseq2 [ 69 ] and EdgeR [ 70 ], two bioinformatics pipelines originally designed for RNAseq analyses. Other Tn-seq analysis tools are now available, such as MAGenTA [ 71 , 72 ], which can track all individual insertions and generate fitness values for each insertion (nucleotide resolution). However, DEseq2 and EdgeR have recently gained acceptance for Tn-seq gene fitness analyses based on their availability and ease-of-use [ 58 , 60 , 73 – 75 ].…”

The landscape of intrinsic and evolved fluoroquinolone resistance inAcinetobacter baumanniiincludes suppression of drug-induced prophage replication

“…Differences in average gene fitness between treated and untreated conditions (W diff ) were considered significant if they fulfilled the following 3 criteria, with minor modification from those previously described (33): per-gene fitness must be calculated from at least 3 data points, the magnitude of W diff must be > 10%, and q value must be < 0.05 in an unpaired t-test with FDR controlled by the 2-stage step-up method of Benjamini, Krieger and Yekutieli (GraphPad Prism 7). Per-insertion fitness scores within a given genomic region were visualized using Integrative Genomics Viewer software (60) after aggregating all scores across multiple independent transposon mutant libraries using the SingleFitness Perl script (61).…”