https://wiki.abi.am/ 2026-04-08T13:42:18+00:00 https://wiki.abi.am/ https://wiki.abi.am/_media/wiki:logo.png text/html 2025-03-25T10:37:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/scripts:adapter_and_quality_trimming?rev=1742899069&do=diff How to perform quality control and adapter trimming of your reads with cutadapt and fastp What to trim Adapters If your FASTQC report shows adapter contamination, remove adapters. There are three common adapters, frequently used in NGS: * Illumina universal adapter (most common): text/html 2025-04-09T12:05:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/scripts:alignment?rev=1744200335&do=diff Align your reads to a reference genome Reference genome index You'll need a reference genome index to align your reads in FASTQ files. There are prebuilt indexes on the ABI server at the following directory: /mnt/db/genomes If you don't find the genome of your interest, you can build the index yourself, by following the steps in the following page [TOWIKI]. text/html 2025-08-06T08:38:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/scripts:download_fastq?rev=1754469492&do=diff Download FASTQ from SRA An easy intro The easiest way to download FASTQ files from SRA is using the fastq-dump command from the SRA Toolkit with the command: fastq-dump --gzip --split-3 SRR[accession ID] Options: ''--gzip'' will compress the downloaded FASTQ files (this is strictly recommended to save space) ''--split3'' will split your files into _1 and _2 files if it's a paired-end sequencing and will store singleton reads (those that don't have a pair) in a separate file. If it's singl… text/html 2025-03-21T12:43:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/scripts:qc?rev=1742561001&do=diff Quality Control with FastQC, Fastp and MultiQC The following scripts perform quality check with FastQC and MultiQC. You can find Fastp in How to perform quality control and adapter trimming of your reads with cutadapt and fastp. Fastp performs quality trimming and also generates reports, which can be used as input to MultiQC. FastQC Uses fastq files as inputs and generates reports. Below daughter and parent scripts are provided. text/html 2025-03-07T11:42:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/scripts:run_job_on_slurm?rev=1741347751&do=diff Using SLURM to run jobs 1. Create an example script named slurm_example.sh: #!/bin/bash #SBATCH --mem 10gb # the amount of memory you request for your job #SBATCH --cpus-per-task=4 # Number of CPU cores per task #SBATCH --output=slurm-%j.log # file name where the job console output will be stored #SBATCH --mail-type=BEGIN,END # if specified you will receive email when your job starts, ends #SBATCH --mail-user=<your_mail> # your email address for i in {1..100..1} … text/html 2025-03-26T09:59:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.abi.am/scripts:start?rev=1742983177&do=diff Bunch of useful scripts are under this namespace, use the Sitemap to see all of them Index of Scripts