Abhimanyu Singh
A bioinformatics beginner
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Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2952 days ago by Jitbowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw...Senior Scientist (Agricultural Bio-informatics) (One post)
Agricultural Scientists Recruitment Board Qualifications Essential: Doctoral degree in Bio-informatics/ Biotechnology/Molecular Biology and Biotechnology/Life Sciences/ Computer Sciences with specialization in Bio-informatics including relevant...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2925 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...RStudio
By Jitendra Narayan 4187 days ago Comments (1)http://www.rstudio.com/ - RStudio IDE is a powerful and productive user interface for R. It’s free and open source, and works great on Windows, Mac, and Linux. The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr,...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2826 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...Research Associate @ TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN...
TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI – 410210 Website: www.actrec.gov.in; Ph: 27405000 No. ACTREC/Advt./ 66 /2014 23rd December, 2014 Research Associate International...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 2366 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...Comparative Genomics in Ensembl
By Rahul Nayak 4162 days agoThe Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences. Learn how to view and export these data in this video.SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2312 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:Bioinformatics Scripts
By Jit 4160 days agomilkweedgenome.org - Some of the useful bioinformatics scripts. For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly. http://milkweedgenome.org/?q=scripts
