BOL

Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner

SAM and BAM handling with Perl http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm # Perl #SAM #BAM

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and...

YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a...

#Download #blastDB #locally. $ wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz" for NT and wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz" for NR

Split the bam file by chromosome. $ bamtools split -in file.bam -reference #Split #Bam #Bamtools

splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...

PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high...

#Contiguous and #accurate de novo #assembly of #metazoan genomes with modest long read coverage https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw654

BioDownloader is a program for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers: optimized to work with vast amount of data...