Surabhi Chaudhary
A Bioinformatician
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BIMA V3: an aligner customized for mate pair library sequencing
By Abhimanyu Singh 3583 days agobioinformatics.oxfordjournals.org - Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...splitbam: splits a BAM by chromosomes
By Jit 3507 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...LoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 3466 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 3196 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2812 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...Understanding HiFi Reads !
By Rahul Nayak 1657 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...Trust But Verify: Sequencing Your Cell Lines Might Reveal an Uninvited Guest
By LEGE 489 days agoHigh-throughput sequencing has become indispensable in cell biology, enabling detailed insights into chromatin structure, gene expression, and regulatory dynamics. Yet, when faced with unexpectedly low mapping rates to the human genome,...HipSTR: Haplotype inference and phasing for Short Tandem Repeats
By BioJoker 2770 days agogithub.com - HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by: Learning locus-specific PCR stutter models using an EM algorithm Mining candidate...dcGOR
By Martin Jones 4350 days agoan R package for analysing ontologies and protein domain annotationsCANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3815 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...
