Assembly and annotation of metagenomics reads from soil samples

Scripts used for analysis of permafrost samples. The workflow included:

1. Running multiassembly

assembly_parallel.pbs

megahit_parallel.sh

2. Filtering out short (i.e., less than 1000 bp) contigs

bioawk -c fastx '{ if(length($seq) > 50) { print ">"$name; print $seq }}' some_seq.fastq

3. Quality checking with QUAST

metaquast contigs1 --threads

4. Annotate the contigs with Prokka

prokka --outdir functional_annotation_multi --prefix $NAME --norrna --notrna --metagenome final.contigs.fa