Genome Assembly Tools and Software - PART1 !!
...s help scientists use optical map data.Once complete, it will e...reference bias as compared to mapping based approaches....ituations that may arise when mapping contigs to the reference...cy of a genome assembly using mapped paired end reads, without...2741 days ago
Quick next generation sequencing (NGS) terms definition
...erefore, in the absence of structural variants, mapping locations of the paired e...a read pair is called concordant if they can be mapped to the reference genome as...ature.split reads: a read that can only be mapped to the reference genome by...2578 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple genomes at...exact repeat somewhere, reads mapping to it will be mapped ambi...is a tool that bins reads by mapping to multiple references si...onella reads)clean.fq (unmapped reads)In this case, "int=t...2370 days ago
PerlOneLiner for Bioinformatician
...ld with its absolute valueperl -alne 'print "@{[map { abs } @F]}"' # Find the to...umber of fields that match a patternperl -alne 'map { /regex/ && $t++ } @...te a random 8 character passwordperl -le 'print map { ("a".."z")[rand 26] } 1..8'...2358 days ago
Installing Bio::SCF perl module
...write.o gzwrite.cgcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOUR...644 "SCF.bs""/usr/bin/perl" "/usr/share/perl/5.22/ExtUtils/xsubpp" -typemap "/usr/share/perl/5.22/ExtUtil...2274 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
...m -d hs37m r1.fq r2.fq > r12.gsnap.sam novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo > r12.novo.sam smalt map -f samsoft -i 650 -o r12.smal...2238 days ago
List of non-commercial NGS genotype-calling software
...ple LD Candidate SNPs, genotype likelihoods Software for imputation and phasing, including a mode for genotype calling. Requires fine-scale linkage map QCall ftp://ftp.sanger.ac.uk...2152 days ago
Frequent parameters for bioinformatics tools !
...ulling_limit 2 -perc_identity 95 blastp (VF) -culling_limit 2 RGI (ABR) --input_type contig bowtie2 (mapping) --sensitive minimap2 (mapping) -a -x map-ont &...1341 days ago