587 days ago
3104 days ago
Computer simulation of genetic mechanism !!
...tions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottl..., employing a minimal set of parameters. http://sammeth.net/confluence/display/si...modifying Hudson's ms software to generate samples of DNA sequences with a b...2972 days ago
Software and Tools to detect structure variation with long reads !!
...utput from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled! Mo...ture" regions Genotyping of SVs with Illumina paired-end reads from WGS samples More at https://g...2604 days ago
3005 days ago
2925 days ago
Genome Assembly Tools and Software - PART2 !!
...set of aligned sequence reads in a SAM file and a set of variant cal...om ultra-deep sequencing of a mixed sample. The package contains prog...m the burdens of data preparation. SAMMate 2.7.4 / assemblySAM 1.1 &...ds by using either a model-based or sampling-based simulation. SIS &...2682 days ago
3943 days ago
Bioinformatics Courses Around the World
...Computational Biology (Newark, New Jersey) Sequence Alignment and Modeling System (Documentation for SAM) Technical University of Den...3940 days ago
3162 days ago
Palindrome Simulation commands !
...Simulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa...o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa...1732 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2180 days ago
Comment on "URMAP, an ultra-fast read mapper"
...ome index filename is given by the -ufi option. A filename for SAM format output is specified by -samout. Use /dev/stdout or "-" (m...reate the file. Example urmap -map reads.fastq -ufi hg38.ufi -samout reads.sam1280 days ago
Comment on "Sibelia: A comparative genomics tool"
...variable or input files are in the same folder with "Sibelia" execut...index numbers of sequences (in the same order as they apper in the i...a synteny block. Copies having the same number in the "tag" field (l...gluing "stripes" consisting of the same synteny blocks. For example,...1282 days ago