Shruti Paniwala
A Bioinformatician
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cutadapt
By Radha Agarkar 3586 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...Anvio
By Shruti Paniwala 3551 days agogithub.com - In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would not have been possible without the help of many people who...WgSim
By Jit 3545 days agogithub.com - Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing...QuIN’s web server
By Jit 3540 days agojournals.plos.org - Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for...Genome Workbench 2.10.7
By Gudiya Pal 3536 days agoGenome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.Bioinformatics tools and software
By Jit 3532 days agodrive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW. UPARSE >OTU clustering for 16S and other marker genes....ONT assembly and Illumina polishing pipeline
By Jit 3026 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 2881 days agogithub.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...EAGLER: a scaffolding tool for long reads.
By Jit 2834 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...Converting a VCF into a FASTA given some reference !
By Jit 2787 days agoconverting a VCF file into a FASTA file given a reference sequence
