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How to run BLAST on a compressed FASTA file

FASTA files with sequences from next-generation sequencing projects can be large and are usually stored as compressed files using compression algorithms such as GZIP or ZIP. If you do not want to extract all the data or create another copy of the file when performing a BLAST search, you can combine the file extraction and the BLAST search using a pipe in Unix-based operating systems and tell the BLAST program to use the standard input. Here is one example on how to do that (assuming you have a GZIP compressed FASTA file):

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How to remove human DNA sequence contamination from metagenomes

The immense amount of metagenomic data produced today requires an automated approach for data processing and analysis. Before any downstream analysis will be performed, the datasets should be preprocessed to ensure the quality of the data and prevent erroneous conclusions. One step of your data preprocessing (usually the last) should be to check for sequence contamination (DNA from sources other than the sample). This post will show you how to identify and remove human sequence contamination from metagenomes, but can also be applied to any other type of sequence dataset or contamination.

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How to convert FASTQ to FASTA

The following examples show how to convert a FASTQ file to a FASTA file. The commands assume a Unix-based operating system with Perl.

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How to create a database for BWA and BWA-SW

The following example shows how to create a database from the human reference genome for the use with BWA, BWA-SW and DeconSeq. The commands used below assume a Unix-based operating system.

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