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This article mainly introduces the use of Bowtie2 and parameters of the example analysis, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor with you to understand.

The steps for segment sequence alignment using bowtie2 are generally as follows:

1. Construction of index for reference sequences

Bowtie2-build genome.fasta index

two。 Sequence alignment

Bowtie2-p 8-x index-1reads1.fq-2 reads2.fq-S out.sam

Required parameters:

-x the prefix of the index file generated by bowtie2-build.

-1 double terminal to find the corresponding file 1. Multiple files can be separated by commas; multiple files must correspond to the files specified in-2.

-2 double terminal to find the corresponding file 2.

-U non-double terminal to find the corresponding file. You can have multiple files separated by commas.

-S generated file prefix in SAM format.

Output parameters:

-t/--time-- un writes unpaired reads to.

-- un-gz writes unpairedreads to gzip compression.

-- un-bz2 writes unpairedreads to bz2 compression.

-- al will be able to match at least one unpairedreads write.

-- al-gz..., gzip compression.

-- al-bz2..., bz2 compression.

-- un-conc writes paired-endreads that cannot be matched harmoniously.

-- un-conc-gz..., gzip compression.

-- un-conc-bz2..., bz2 compression.

-- al-conc will be able to harmoniously compare paired-endreads writes at least once.

-- al-conc-gz..., gzip compression.

-- al-conc-bz2..., bz2 compression.

Sam parameters:

-- no-unal does not record reads that is not matched.

Performance parameters:

-p/--threads NTHREADS sets the number of threads. Default: 1

Reorder multithreaded operation, the order of the alignment results will be inconsistent with the order of the reads in the file, using this option, it will be consistent.

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