BOL

#Clustering metagenomic #contigs on #tetranucleotide frequency http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html

MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. More...

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component...

Convert a SAM file to tab-delimited alignment coordinates https://gist.github.com/sjackman/7016520 #SAM #BAM #Convert #Tab

Understanding MegaBlast https://gordonlab.wustl.edu/btheta/blast/docs/megablast_readme.html #Blast #BLASTn #MegaBlast #Alignment

Whole-Genome Sequencing (WGS) PPT http://www.bx.psu.edu/~ratan/Sequence%20Analysis.pdf #PPT #WGS #Ratan

If you have > Blast 2.2.29 versions, then you need to put -max_hsps 1 parameter, and it gonna work well for you. 

I used the following command to print the blast hit. [Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out...

SAM flags https://broadinstitute.github.io/picard/explain-flags.html #SAM #Flags