BASH script for SelfBLAST a genome
...n echo "You want entire sequence to blast" SEQ=$FASTAFILE else echo "Something went wrong $USER - Contact jitendra" fi echo "Doing alignments -- BLASting"; blastn -task m...2615 days ago
2089 days ago
Installing Porechop on Ubuntu !
...be searched for adapter sequences (default: 150) --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ign...2069 days ago
2038 days ago
To convert just one specific read group to fastq
...bam/*.bam # Investigate the readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam echo "" echo "Number of alignments with read group: GROUP-SRR197...1505 days ago
913 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam781 days ago
Script to rapid genome clustering based on pairwise ANI
...-db -outfmt '6 std qlen slen' -max_target_seqs 10000 -perc_identity 90 -o -num_threads 32 Next, calculate pairwise ANI by combining local alignments between sequence pairs: anica...598 days ago