Computer simulation of genetic mechanism !!
...popgen MetaSim A tool to generate collections of synthetic reads that reflect the diverse taxo...goldman-srv/phylosim/ pIRS Profile-based Illumina pair-end reads simulator https://code.google...2968 days ago
2796 days ago
Structural variation: the hidden genomic treasure
...detection in next generation sequencing data (paired end mapping, split reads, and depth of coverage), arra...ructuralVariants.pdfBreakSeq, structural variant genotyping using split reads Link CopySeq, genot...2696 days ago
Software and Tools to detect structure variation with long reads !!
...ntification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp...ey considers both intra-read discordance and soft-clipped tails of long reads to identify structural varian...2601 days ago
String graph based genome assembly software and tools !
...ses. The first phase corrects base calling errors in the reads. The second phase assembles contigs from the corrected reads. The third phase uses paired...howing practical advantages in running FSG on multiple threads. Moreover, we have studied th...2322 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
...3/bwa GraphMapMapper for long and error-prone readshttps://github.com/isovic/grap...nlr/LINKS/ marginAlignTools to align nanopore reads to a referencehttps://github....of assemblers for Oxford Nanopore MinION long reads LQSDALIGNER, Celera OLC Nano...2314 days ago
BBTools for bioinformatician !
BBMap.sh Mapping Nanopore reads BBMap.sh has a length cap of 6kbp. Reads longer than this will be brok...GGGAAAAA In this case, all reads starting with "AAAAACCCCCTTTT...ault, "filterbyname" discards reads with names in your name list,...2264 days ago
2126 days ago
Understating pacbio reads name !
...Part Number (usually "p0", "X0" when using expired reagents) ZMW hole number Subread Region (start_stop using polymerase read coordinates) readScore barcodeScore...1983 days ago
Understanding reads mapping and flags !
...by the supplementary alignment flag. Chimeric reads are indicative of structural...ric genes in RNA-seq. In short, chimeric reads can be split in to two or mor...that GATK can realignment those representative reads to the correctly position via...1830 days ago