Changes in version 1.1.4 o bowtie2 version updated to 2.4.4 o Able to build large bowtie indexes (.bt21) o Able to align against large bowtie indexes (.bt2l) o Able to create bam alignment files o Use the bowtie2 and bowtie2-build wrapper scripts rather than the binaries directly Changes in version 1.0.0 INITIAL RELEASE o bowtie2 version 2.3.2 o AdapterRemoval version 2.2.1a