Jit
Enthusiast computational biologist with business dream !!!
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Nicolas Corradi Lab
The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance. To achieve this goal, our team combines the power of next generation DNA sequencing and...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2997 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2849 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2683 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Staff Scientists at National Institute of Plant Genome Research, New Delhi
National Institute of Plant Genome Research, New Delhi is an Autonomous Research Institution funded by Department of Biotechnology, Ministry of Science & Technology, Govt. of India, to pursue research on various aspects of plant genomics. The...Pilon
By Rahul Nayak 3832 days agogithub.com - Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads...Advanced Bash-Scripting Guide
By Jit 3823 days agotldp.org - This tutorial assumes no previous knowledge of scripting or programming, yet progresses rapidly toward an intermediate/advanced level of instruction . . . all the while sneaking in little nuggets of UNIX® wisdom and lore. It serves as a...Picard
By Neel 3752 days agobroadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...Sequence assembly with MIRA 4
By Priya Singh 3775 days ago Comments (1)mira-assembler.sourceforge.net - MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by electrophoresis sequencing (aka Sanger sequencing) 454 pyro-sequencing (GS20, FLX or Titanium) Ion...Understanding Fastqc Output
By Jit 3766 days agowww.bioinformatics.babraham.ac.uk - Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at...
