2/15/2022

Download TagNotate For Mac 2.0.4

  • Very useful and reliable package, it makes robust analysis but at the same time it´s easy to understand and especially to use. It has many functions so it covers 95% of the required steps to find sequence variants. I must say that honestly the tutorial is one of the few that is really well written and that that explains how to make the analysis step by step. You can go throughout it easily without previous knowledge and still be able to complete the whole SNPs identification and annotation. Additionally it has a very good balance between speed and reliable results.
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  1. TagNotate 2.0.4 for Mac is available as a free download on our software library. Our built-in antivirus checked this Mac download and rated it as 100% safe. The program is included in Productivity Tools. The actual developer of this Mac application is Tim and Gerry Inc.
  2. OVF: fixed import of OVFs with a VM description (annotation) (3.2.2 regression; bug #6914) VRDP: fixed issues with secondary monitors (bug #6759) VirtualBox 3.2.4 Screenshots.

Introduction

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

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Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).

The main processing of such FASTA/FASTQ files is mapping (aka aligning)the sequences to reference genomes or other databases using specializedprograms. Example of such mapping programs are: Blat, SHRiMP,LastZ,MAQ and many many others.

However,
It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results.

The FASTX-Toolkit tools perform some of these preprocessing tasks.

Available Tools

  • FASTQ-to-FASTA converter
  • FASTQ Information
    Chart Quality Statistics and Nucleotide Distribution
  • FASTQ/A Collapser
    Collapsing identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)
  • FASTQ/A Trimmer
    Shortening reads in a FASTQ or FASTQ files (removing barcodes or noise).
  • FASTQ/A Renamer
  • FASTQ/A Clipper
    Removing sequencing adapters / linkers
  • FASTQ/A Reverse-Complement
    Producing the Reverse-complement of each sequence in a FASTQ/FASTA file.
  • FASTQ/A Barcode splitter
    Splitting a FASTQ/FASTA files containning multiple samples
  • FASTA Formatter
    changes the width of sequences line in a FASTA file
  • FASTA Nucleotide Changer
  • FASTQ Quality Filter
    Filters sequences based on quality
  • FASTQ Quality Trimmer
  • FASTQ Masker
    Masks nucleotides with 'N' (or other character) based on quality

These tools can be used in two forms:
  1. Web-based (with Galaxy).
    Galaxy's Test website already contains some of the FASTX-toolkit tools.
  2. Command-line:
    running the tools from command line (or as part of a script).

Tools demonstration

Visit the Hannon lab public galaxy server to see a demonstration of these (and other) tools.

News

Download TagNotate For Mac 2.0.4

02-Feb-2010 - Version 0.0.13

New tools:
fastq_masker (suggested by Ben Bimber)
New features:
fastx_trimmer can trim N nucleotides from the end of the sequences (a new command line option, and a separate tool in Galaxy)Professional
fastx_clipper accepts minimum adapter length to clip (requested by Erick Antezana, command line only)
Improved Galaxy integration:
Almost all tools have working functional tests (except the plotting tools and barcode splitter).
Mac Plotting tools (nucleotide distribution and quality boxplot) detect input file type and show a detailed warning if given a FASTA/Q file as input
(hopefully reducing bug reports).
Tools read the input FASTQ type (sanger or solexa) and use the correct quality ASCII offset (33 for sanger, 64 for solexa).

Dec-2009 - Version 0.0.12

never officially released

24-Nov-2009 - Version 0.0.11

New tools: fastx_uncollapser, fastq_quality_filter.
New features: fastx_collapser can re-collapse an already-collapsed FASTA file; fastx_trimmer can trim N bases from the end of the sequence.
Minor compilation bug-fixes.

10-Aug-2009 - Version 0.0.10

Download TagNotate For Mac 2.0.4Bug fix on Mac OS X (reported by Joshua Waterfall).
New tool: FASTX-Renamer (based on suggestion+patch by Charles Plessy).Download
New undocumented command line argument: -Q NN handles FASTQ ASCII quality with user specified offset (was hard-coded as 64 in previous versions). Requested by Erick Antezana
Barcode-Splitter: improved galaxy integration - stores output files directly into galaxy's files database; no need for external webserver anymore.
Uses libgtextutils-0.5 library (as a dynamic library)

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Version 0.0.9

Never released.

12-Mar-2009 - Version 0.0.8

Minor changes to compilation stage, as suggested by users.
FASTX-toolkit should now compile cleanly on Mac OS x.
No new features were added.
Using libgtextutils-0.3 library.

24-Mar-2009 - Version 0.0.7

Added Fasta-Formatter and Fasta-Nucleotide-Changer

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tools.
Using

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libgtextutils-0.1 library.

25-Feb-2009 - Version 0.0.6

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Initial public release.