Results for "PacBio read correction"
Top-level pages
Installing Bio::SCF perl module
Most Perl modules are written in Perl, some use XS (th...OURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.cgcc -O3 -D_LARGEFILE64_SOURC...look for a library named "libread". jitendra@jitendra-UNLOCK-I.... -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I...2271 days ago
- To remove all line ends (\n) from a Unix text file: sed ':a;N;$!ba;s/\n...text file: cat file_list.txt | while read line; do cp "$line" complete_...es into sets with mapped and unmapped reads: samtools view -F4 sample.b...ut -d' ' -f1 < your_file To count reads in a...
2270 days ago
- $ sudo apt-get install python-numpy python-scipy python-matplotli...-nose[sudo] password for urbe: Reading package lists... DoneBuilding dependency tree Reading state information... DoneT...lected package python-pymysql.(Reading database ... 435155 files...'w' at 0x7f85d1de31e0>, longreads=[],...
2243 days ago
Parallel Processing with Perl !
Here is a small tutorial on how to make best use of multiple proces...is. One best way is using perl threads and forks. Knowing how these threads and forks work is very impor...ards using perl fork than perl threads. One of the oldest way to f...ax_processors);while (my $file = readdir(DI...2132 days ago
- It's been a while since I last installed BLAT and when I went to the download directory at UCSC: http://u...ectory blatSrc now move into that directory. #cd blatSrc before you begin read the README fil...
2116 days ago
Frequent parameters for bioinformatics tools !
Third party executable parameters and options. Trimmomatic...reen --aligner bowtie2' (bwa for PacBio) --subset 1000 (for PacBio) SPAdes --careful...Pbalign.task_options.no_split_subreads: false Genomic_consensus.ta...6000000 Pbcoretools.task_options.read_lengt...1338 days ago
- Follow this: Settings file Error Your web server does not have permission to create t...his message: Welcome Installing Elgg has 6 simple steps and reading this welcome is the first one! If you haven't already, rea...
945 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this...a as we used above: illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reverse reads A...878 days ago
- Short Read Simulators With the popularity of next-generation sequ...below are some popular short read simulators. Links to their pu...tly, many of the popular long read simulators are designed to si...(1) Pacific Biosciences (PacBio) and (2) Oxford N...pular and recently introduced PacBio and...
636 days ago
Bioinformatics tools for genome assembly !
There are numerous genome assembly tools available, each with its...assembler optimized for short-read sequencing data. SOAPdenov...ologies, such as Illumina and PacBio. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequenc...extension of SPAdes for long-read data,...339 days ago
