Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
: Bwa
suggests : bowtie2
Please refer to the [bowtie1 manual] for more detailed information.
The code used to be downloaded from sourceforge https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1[1] but recently moved to GitHub https://github.com/BenLangmead/bowtie [2]
Current version of the Illumina's iGenomes cufflinks annotation files were obtained (here: [3]) and is documented (here: [4]). Importantly, These annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis.
References:
- ↑ https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1
- ↑ https://github.com/BenLangmead/bowtie
- ↑ http://cufflinks.cbcb.umd.edu/igenomes.html
- ↑ ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt
