update README

Author: MikkelSchubert

README.md

@@ -11,6 +11,16 @@ not available.
 For questions, bug reports, and/or suggestions, please use the
 [GitHub tracker](https://github.com/MikkelSchubert/adapterremoval/issues/).
 
+# AdapterRemoval v3 - Dang fast(Q) processing
+
+AdapterRemoval v3 is a major revision of AdapterRemoval, that aims to simplify usage by picking a sensible set of default settings, adding new features to handle a wider range of data, providing [human readable HTML reports](https://mikkelschubert.github.io/adapterremoval/examples/example.html) and machine [readable JSON files](https://mikkelschubert.github.io/adapterremoval/examples/example.json), as well as greatly improving overall throughput.
+
+AdapterRemoval v3 is still a work in progress, but alpha release 2 is [available for download](https://github.com/MikkelSchubert/adapterremoval/releases/tag/v3.0.0-alpha2/). Documentation is available at [Read the Docs](https://adapterremoval.readthedocs.io/en/v3.0.0-alpha2/), including a guide on how to migrate from v2. Bug reports, feature requests, and other feedback is greatly appreciated.
+
+Compiling AdapterRemoval v3 requires [libdeflate](https://github.com/ebiggers/libdeflate), [isa-l v2.30+](https://github.com/intel/isa-l), and a compiler with support for C++17. AVX512 support requires GCC v11, Clang v8, or later. Apple M1 is currently not supported.
+
+# AdapterRemoval v2
+
 If you use AdapterRemoval v2, then please cite the paper:
 
     Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter
@@ -23,20 +33,18 @@ AdapterRemoval was originally published in Lindgreen 2012:
     Sequencing Reads, BMC Research Notes, 5:337
     http://www.biomedcentral.com/1756-0500/5/337/
 
-
 ## Overview of major features
 
- - Trimming of adapters sequences from single-end and paired-end FASTQ reads.
- - Trimming of multiple, different adapters or adapter pairs.
- - Demultiplexing of single or double indexed reads, with or without trimming
+- Trimming of adapters sequences from single-end and paired-end FASTQ reads.
+- Trimming of multiple, different adapters or adapter pairs.
+- Demultiplexing of single or double indexed reads, with or without trimming
    of adapter sequences.
- - Reconstruction of adapter sequences from paired-end reads, by the pairwise
+- Reconstruction of adapter sequences from paired-end reads, by the pairwise
    alignment of reads in the absence of a known adapter sequence.
- - Merging of overlapping read-pairs into higher-quality consensus sequences.
- - Multi-threading of all operations for increased throughput.
- - Reading and writing of gzip and bzip2 compressed files.
- - Reading and writing of interleaved FASTQ files.
-
+- Merging of overlapping read-pairs into higher-quality consensus sequences.
+- Multi-threading of all operations for increased throughput.
+- Reading and writing of gzip and bzip2 compressed files.
+- Reading and writing of interleaved FASTQ files.
 
 ## Documentation
 
@@ -45,7 +53,6 @@ the [online documentation](https://adapterremoval.readthedocs.io/). A summary
 of command-line options may also be found in the manual page, accessible via
 the command "man AdapterRemoval" once AdapterRemoval has been installed.
 
-
 ## Installation
 
 ### Installation with Conda
@@ -54,7 +61,6 @@ If you have `Conda`_ installed on your system:
 
     conda install -c bioconda adapterremoval
 
-
 ### Installing from sources
 
 Installing AdapterRemoval from sources requires libz and libbz2.
@@ -72,7 +78,6 @@ subdirectory and may be installed by running "make install":
 
     sudo make install
 
-
 ## Getting started
 
 To run AdapterRemoval, specify the location of pair 1 and (optionally) pair 2
@@ -81,8 +86,7 @@ FASTQ using the --file1 and --file2 command-line options:
     AdapterRemoval --file1 myreads_1.fastq.gz --file2 myreads_2.fastq.gz
 
 By default, AdapterRemoval will save the trimmed reads in the current working
-directly, using filenames starting with 'your_output'. 
-
+directly, using filenames starting with 'your_output'.
 
 More examples of common usage may be found in the
 [Examples](https://adapterremoval.readthedocs.io/en/latest/examples.html)