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[ci skip] README update
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Jeremiah Wala committed Sep 5, 2016
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Other C++ APIs
------------------------------
There are overlaps between this project and the [BamTools][BT] project from Derek Barnett, the [Gamgee][gam]
project from the Broad Institute, and the [SeqAn][seqan] library from Freie Universitat Berlin. These projects
provide excellent and high quality APIs. SeqLib provides further performance and capabilites for certain classes of
bioinformatics problems, without attempting to replace these projects.

SeqLib provides some overlapping functionality (eg BAM read/write) but in many cases with improved performance (~2x over BamTools).
SeqLib further provides in memory access to BWA-MEM, a chromosome aware interval tree and range operations, and to read correction and
sequence assembly with Fermi. BamTools has more support currently for network access and multi-BAM reading. SeqAn provides
additional capablities not currently supported in SeqLib, including graph operations and a more expanded suite of multi-sequence alignment
tools (e.g. banded Smith-Waterman). Gamgee provides similar functionality as a C++ interface to HTSlib, but does not incorportate BWA-MEM or Fermi.
SeqLib is under active development, while Gamgee has been abandoned.
There are overlaps between this project and [BamTools][BT] from Derek Barnett, [Gamgee][gam]
from the Broad Institute, and [SeqAn][seqan] from Freie Universitat Berlin. These projects
provide excellent and high quality APIs. SeqLib provides further performance enhancement and new capabilites for certain classes of
bioinformatics problems.

Some differences:
1. SeqLib has ~2-4x faster read/write speed over BamTools and SeqAn, and lower memory footprint.
2. SeqLib has support for CRAM file
3. SeqLib provides in memory access to BWA-MEM, BLAT, a chromosome aware interval tree and range operations, and to read correction and
sequence assembly with Fermi. BamTools has more support currently for network access.
4. SeqAn provide a substantial amount of additional capabilites not in SeqLib, including graph operations and a more expanded suite of multi-sequence alignments.
5. BamTools has support for network access of BAMs.

For your particular application, our hope is that SeqLib will provide a comprehensive and powerful envrionment to develop
bioinformatics tools. Feature requests and comments are welcomed.
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