Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Workflow

1. Input paired-end reads
   Upload paired-end FASTQ files, including R1 and R2 reads.

2. Select host reference index
   Use a pre-built Bowtie2 host genome index, such as human GRCh38.

3. Align reads to host genome
   Run Bowtie2 in sensitive end-to-end mode to map reads against the host reference genome.

4. Extract non-host reads
   Reads that do not align concordantly to the host genome are retained as non-host clean reads.

5. Generate summary results
   Output filtered FASTQ files and a host-filtering summary table reporting total read pairs, host-mapped pairs, and non-host pairs.

Data

Example dataset include 100 bp illumina WGS reads consist of ~10% subsets of 3 paired end sets of reads from the following publication:
The sample names in the original publication used to generate the toy dataset is ERR260162 (sample1)

Result：

v1.4:The pipeline is stored in Code Repository: CRS1233581760978366464. The computational docker enrionment is stored in Software Repository: SRS1233582345840504832.
Reference data is stored in Data Repository:
DRS1233531493054427136

Reproducibility

The pipeline utilizes code CRS1233581760978366464 and Docker image SRS1233582345840504832 and Reference Data DRS1233531493054427136, all of which are stored in the BMAP repositories.

Usage

1. Select the application 'Bowtie2 filtering human'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters(Reference data)
5.Click Add option and fill in actual test data

6. Upload the compressed data in gz or rar format.