title: Metagenome of mus musculus colon: stressed mice
design: Sequencing adapters were removed from sequencing reads using cutadapt v1.9. Low quality reads were trimmed by fqtrim v0.94 using a sliding-window algorithm. Reads were aligned to the host genome using bowtie2 v2.2.0 to remove host contamination. Quality-filtered reads were de novo assembled to construct the metagenome for each sample by IDBA v1.1.1. All coding regions of metagenomic contigs were predicted by MetaGeneMark v3.26. Coding region sequences of all samples were clustered by CD-HIT v4.6.1 to obtain unigenes. Unigene abundance for a certain sample was estimated by TPM based on the number of aligned reads by bowtie2 v2.2.0.  The lowest common ancestor taxonomy of unigenes was obtained by aligning them against the NCBI NR database by DIAMOND v0.0.14. Functional gene annotation and pathway mapping was conducted with the KEGG database
library_name: SD163