Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:config auto_version auto_he...2271 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner +...indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is python...2087 days ago
Long reads mapper bash script !
.../bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minima...echo "Name of the file used for mapping $fileName, present at $refFas...olName == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLo...Name == "ngmlr" ]; then echo "Mapping with $toolName" if [ $reads...2085 days ago
2086 days ago
1797 days ago
Bash script to alignment of short reads against reference genome !
...s: sambamba markdup SRR1770413.raw.sorted.bam SRR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same cr...1522 days ago
Installing docker for Bioinformatics on Ubuntu !
...logs Fetch the logs of a container pause Pause all processes within one or more containers port List port mappings or a specific mapping for the container ps...1476 days ago
830 days ago