Contamination checking for fasta/fastq files

fastq2blast.sh

export BLASTDB=/data/public_data/NCBI/NCBI_all/ #and specify the db as -db nt |or -db /data/public_data/NCBI/NCBI_nt/nt
export PATH=/applications/UCSC-tools/:/applications/ncbi-blast+/ncbi-blast-2.2.30+/bin/:$PATH

#subsetting and converting into fasta
file=sample.fq.gz
filefa=${file%.fq.gz}_subset.fa
n=400000
zcat $file | head -n $n > ${file%.fq.gz}_subset.fq
fastqToFa ${file%.fq.gz}_subset.fq $filefa

#blasting and summarizing

#filefa=file.fa 
blastn -num_threads 10 -evalue 0.001 -outfmt '7 std scomnam sacc staxids qacc sallseqid sallgi sscinames scomnames sblastnames sskingdoms salltitles' -num_alignments 5 -db nt -query $filefa -out ${filefa}.blast
#head ${filefa}.blast
# BLASTN 2.6.0+
# Query: NB501820:38:H22JFAFXY:1:11101:22479:1239 2:N:0:GGACTCCT
# Database: nt
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, subject acc., subject tax ids, query acc., subject ids, subject gis, subject sci names, subject com names, subject blast names, subject super kingdoms, subject titles
# 5 hits found
#NB501820:38:H22JFAFXY:1:11101:22479:1239        NG_054891.1     97.260  73      2       0       1       73      4356    4284    1.70e-25    124     NG_054891       9606    NB501820:38:H22JFAFXY:1:11101:22479:1239        gi|1198817830|ref|NG_054891.1|  1198817830 Homo sapiens     human   primates        Eukaryota       Homo sapiens integrin subunit beta 1 binding protein 2 (ITGB1BP2), RefSeqGene on chromosome X
#NB501820:38:H22JFAFXY:1:11101:22479:1239        NG_046742.1     97.260  73      2       0       1       73      22439   22367   1.70e-25    124     NG_046742       9606    NB501820:38:H22JFAFXY:1:11101:22479:1239        gi|1000814597|ref|NG_046742.1|  1000814597 Homo sapiens     human   primates        Eukaryota       Homo sapiens non-POU domain containing octamer binding (NONO), RefSeqGene on chromosome X

less ${filefa}.blast | sort -u -k1,1 --merge | grep -v "# BLAST" | cut -f19 | sort | uniq -c | sort -r -n > ${filefa}.blast.processed 
#head ${filefa}.blast.processed
#      2 human
#      1 house mouse