Release note

Written by Marko Marinkovic in

on October 30th, 2023

The pRESTO 0.7.1. toolkit is the latest new toolkit addition in our Public Apps gallery. It includes the following apps: 

• ParseLog – Parses pRESTO log records and outputs values in TAB-separated tables. 
• BuildConsensus – Builds consensus sequences. 
• ClusterSets – Clusters sequences into groups. 
• CollapseSeq– Removes duplicates sequences from input FASTA/FASTQ files. 
• PairSeq – Sorts and matches sequences across input files. 
• ConvertHeaders – Converts sequence headers to pRESTO format. 
• AlignSets – Aligns sequences using different methods. 
• FilterSeq – Filters input sequences. 
• ParseHeaders – Manipulates sequence headers. 
• SplitSeq – Splits and samples sequence files. 
• UnifyHeaders – Reassigns or deletes sequence header fields. 
• AssemblePairs – Assembles paired-end reads to a single sequence. 
• MaskPrimers – Removes primers and annotates sequences with primers and barcodes. 
• EstimateError – Estimates annotation set error rates.  

We also published the following new tools: 

• ComBat-seq (sva 3.35.2), an R tool used for batch effect adjustment in bulk RNA-seq data. Some additional improvements to the tool wrapper were developed, like removing more than one batch by dataset and adapting outputs to be compatible with downstream analyses (DeSeq). 
• GffRead (0.12.7) GFF/GTF utility tool providing format conversions, filtering, FASTA sequence extraction, and more. 

We published the following updates in our Public Apps gallery: 

• RNA-seq alignment – STAR (2.7.10a), a workflow that performs the first step of RNA-seq analysis – alignment of the reads to a reference genome. It is used to generate aligned BAM files (in genome and transcriptome coordinates) from RNA-seq data, which can later be used in further RNA studies, like gene expression analysis. 
• Trim Galore! (0.6.10) is a wrapper around adapter trimming and quality control tools Cutadapt and FastQC with extra functionality for RRBS data.