Release notes - October 30, 2023
about 1 year ago by Marko Marinkovic
Recently published apps
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.
Recently updated apps
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.